Microbiology General

8/9/2019 Microbiology General

http://slidepdf.com/reader/full/microbiology-general 1/64

MICROBIOLOGY IN THE BIOLOGICAL WORLD

This text provides an introduction to microbiology with a discussionof significant milestones that have been important in the development of microbiology. It also defines new directions for microbiologists of thefuture. The concepts of cell theory and cellular types are introduced alongwith a description of the origin of eukaryotic cells. The informationconcludes with a description of the various members of the microbial worldand how we name them.

KEY CONCEPTS1. Microorganisms have determined the course of history because of the

diseases they cause.2. New infectious diseases appear as lifestyles change people travel to

exotic places and techni!ues for growing and identifying organismsand viruses improve.

". #ells are the basic units of life and all cells must carry out the samecritical functions in order to survive.

$. Two ma%or types of cells exist& the prokaryotes which do not contain a'true' nucleus or other membrane(bound internal structures and theeukaryotes which do contain a true nucleus.

). The microbial world consists of prokaryotes and eukaryotes as well asnon(living agents the viruses and viroids.

*. +ll bacteria are prokaryotes and can be further divided into two largegroups based on their chemical compositions.

SUMMARYI. Introduction+. Microorganisms are in large part responsible for determining the courseof human history.,. The use of modern sanitation facilities vaccinations as well asantibiotics has dramatically reduced the incidence of infectious disease.II. Microorg ni!"! Di!co#$r$d

+. +nton van -eeuwenhoek discovered microorganisms over " years ago by viewing water samples through lenses that magnified three hundredfold.,. The theory of spontaneous generation was revived with the discovery ofthe microbial world.

1. /iffering results from different investigators lead to the controversyof whether living organisms could arise from dead organic matter. Thiscontroversy was not resolved until the 10* s.2. asteur demonstrated that the air is filled with microorganisms andshowed that swan(necked flasks containing sterile infusions could

remain sterile indefinitely.



2. The two groups are not closely related to each other or to theeukaryotes./. =ubacteria include most bacteria familiar to microbiologists.

1. This group is very diverse.2. The 'typical' bacteria which include both eubacteria and

archaebacteria are the most common and although they are alsoheterogeneous they do share some obvious properties.=. +rchaebacteria often grow under extreme conditions of temperature andsalinity./. M$"&$r! o- t*$ Micro&i % Wor%d+. The members include all unicellular organisms which includes all

prokaryotes.,. +lgae fungi and proto9oa are the eukaryotic members of the microbialworld.#. ?iruses viroids and prions are non(living members of the microbialworld./I. No"$nc% tur$ o- Org ni!"!+. +ll organisms are named according to the binomial system of genus andspecies.,. Names and descriptions of most bacteria are published in ,ergey4sManual of 5ystematic ,acteriology.

0 . BIOCHEMISTRY O, THE MOLECULES O, LI,ETo understand how microorganisms live and die produce disease and

do all of the other ama9ing things they do re!uires some workingknowledge of chemistry. This chapter presents the fundamental concepts of the chemistry of living organisms. It starts with the atom the simplest levelof organi9ation and moves to higher levels finishing with themacromolecules. The structure and function of proteins polysac( charidesnucleic acids and lipids are described.

KEY CONCEPTS1. @our elements carbon oxygen hydrogen and nitrogen make up over 30A of all living matter. Two other elements phosphorus and sulfur arealso very important.2. The bonds that hold atoms together result from electrons interactingwith each other. ,onds vary in strength and in the arrangement of electrons which gives molecules characteristic properties.". Beak bonds are important in biological systems since they oftendetermine the most important properties of the molecules and are

responsible for their proper functioning.



$. +ll life is based on the bonding properties of water which comprisesover 3 A of the cell4s weight.). Macromolecules consist of many repeating subunits each subunitconsisting of a small simple molecule. The subunits are firstsynthesi9ed then bonded together to form the macromolecule.

SUMMARYI. E%$"$nt! nd Ato"!+. +n element is a pure substance that consists of a single type of atom.+toms are the basic units of all matter.They consist of three ma%or components& electrons protons and neutrons.II. ,or" tion o- Mo%$cu%$!1 C*$"ic % Bond!+. #hemical bonds are of two types& strong and weak. The stronger the

bond the more energy is re!uired to break it.,. 5trong bonds are usually covalent bonds formed when atoms shareelectrons to fill their outer shell and thereby achieve maximum stability.

1. #ovalent bonds vary in their distribution of shared electrons whichresults in the molecule having a positive and negative charge at differentsites.#. Ionic bonds are formed by the loss and gain of electrons between atoms.In a!ueous solutions they are weak./. 7ydrogen bonds are weak but biologically very important. They hold thetwo strands of /N+ together and are important in determining the shape of

proteins. 1. They result from the attraction of positively charged 7 atoms tonegatively charged N or atoms.III. I")ort nt Mo%$cu%$! o- Li-$+. 5mall molecules in the cell are both organic and inorganic.

1. The inorganic molecules include many that are re!uired for en9yme function.

2. 6rganic molecules are mainly compounds that are beingmetaboli9ed or molecules that are the

subunits of macromolecules.,. +ll very large molecules in the cell :macromolecules< consist of repeatingsubunits called monomers.

1. There are three important macromolecules. roteins are chains ofamino acids that form a polypeptide.

olysaccharides are chains of monosaccharides that form branchingstructures. Nucleic acids are /N+ and ;N+ which are chains ofnucleotides.#. roteins are polymers of amino acids.



1. +mino acid. #onsists of a molecule with a carboxyl group and anamino group bonded to the same carbon atom. The carbon atom is bonded toa side chain. Twenty different amino acids each differing in their sidechains are present in proteins. 2. eptide bond synthesis. + covalent bond is formed between theamino group of one amino acid and the carboxyl group of the ad%acentamino acid with the removal of 767 :dehydration synthesis<. ". -evels of protein structure. Three features characteri9e a protein&:1< its primary structure :2< its shape whether globular or long fibers and:"< whether or not the protein consists of one or several polypeptide chains.+ variety of weak bonds are involved in maintaining the three(dimensionalshape of proteins. $. 5ubstitute proteins contain covalently bonded molecules other thanamino acids. These include glycoproteins :sugars< and lipoproteins :lipids<./. olysaccharides are polymers of monosaccharide :carbohydrate<subunits. #arbohydrates :sugars< contain a large number of alcohol groups:(67< in which the # atom is also bonded to an 7 atom to form 7(#(67.

1. Monosaccharides are the subunits of polysaccharides. The mostcommon are pentoses :)#< and hexoses :*#<.

2. /isaccharides are two monosaccharides %oined together with aloss of water :dehydration synthesis<.

". /ifferent polysaccharides vary in si9e their degree of branching

bonding of monosaccharides to one another and the monosaccharidesinvolved.=. Nucleic acids which include deoxyribonucleic acid :/N+< andribonucleic acid :;N+< are polymers of nucleotide subunits and areunbranched.

1. /N+. The nucleotides are composed of three units& a nitrogen base Cpurine :adenine or guanine< or pyrimidine :thymine or cytosine<Dcovalently bonded to deoxyribose which in turn is bonded to a phosphatemolecule. + phosphate bonded to the sugar molecule %oins the nucleotides

together. /N+ occurs in the cell as a double(stranded helix in which the twostrands are held together by hydrogen bonding between adenine andthymine and between guanine and cytosine.

2. ;ibonucleic acid :;N+<. Nucleotides are the same as in /N+except that ribose replaces deoxyribose and uracil replaces thymine. ;N+ isshorter in length and does not occur as a double helix. Three different typesof ;N+ exist in the cell.@. -ipids are biologically important but are too small and heterogeneous to

be considered macromolecules.



1. +ll lipids have one property in common8they are insoluble inwater but soluble in organic solvents.This difference in solubility is due to their nonpolar hydrophobicnature.

2. They are not composed of similar subunits but rather of a variety of substances that differ in chemical structure.

". 5imple lipids which contain only # 7 and include fats andsteroids. @ats are composed of glycerol covalently bonded to fatty acids.5teroids have a four(membered ring structure.

$. #ompound lipids contain fatty acids and glycerol and in additionoften elements other than # 7 and . They include phospholipidslipoproteins and lipopolysaccharides. They all play important roles inthe cell envelope of bacteria.

). hospholipids consist of two parts each with different properties.6ne end is polar and therefore is soluble in water. The other endcontaining only # and 7 is nonpolar and therefore insoluble in water

but soluble in organic solvents.

2. ,UNCTIONAL ANATOMY O,PROKARYOTES AND EUKARYOTES

This chapter compares and contrasts the functional anatomy of prokaryotic and eukaryotic cell types. The emphasis is on the prokaryoticcell as represented by the bacteria. The functional anatomy consists of adescription of the structure and function of various cellular components./ifferences between prokaryotic and eukaryotic cellular structures serve asthe basis for the selective action of certain antibiotics. rokaryoticorganisms also have several uni!ue structures as well as a metabolicallyinactive endospore.

KEY CONCEPTS

1. The effectiveness of a microscope is based on its ability to visuallyseparate two ob%ects that are close together.2 The many different microscopes that have been developed differ primarilyin their lenses and their method of illuminating the specimen being studied.". +ll bacteria must be able to carry out the functions re!uired for life andtheir small cells must therefore contain the structures to carry out thesefunctions.$ The composition of the rigid bacterial cell wall determines various

properties of the organism including its susceptibility to penicillin and its

staining characteristics



) The cytoplasmic membrane largely determines what material gets into andout of the cell.* In bacteria /N+ occurs as a covalently closed circular molecule withouta surrounding membrane.

The structure ofribosomes differs in eukaryotic and prokaryotic cells> forthis reason some antibacterial medicines such as streptomycin kill

bacteria but are harmless for human cells.0. 5ome bacteria can develop into endospores a type of cell that can survive

adverse conditions such as high temperatures.SUMMARY

I. Micro!co)$ T$c*ni3u$!1 In!tru"$nt!+.The simple microscope has one magnifying lens.,.The compound microscope has two sets of magnifying lenses theob%ective lens and the ocular lens. The magnification is the product of themagnification of the individual lenses.

1. ;esolving power determines the usefulness of a microscope andthe amount of detail that can be seen. It depends on the wavelength ofthe illuminating material.#.The contrast between cells and surrounding medium must be increased toclearly see bacteria/.Types of microscopes

1. hase contrast microscope8a light microscope that increases the

contrast between the bacteria and the surrounding medium.2. Interference microscope8the specimen is viewed in three

dimensions.". /arkfield microscope8the ob%ect being viewed is brightly

illuminated against a dark background.$. @luorescence microscope8ob%ects that fluoresce are visuali9ed

by this light microscope.). The electron microscope can resolve ob%ects a thousand times

better than the light microscope because it uses electrons rather than light to

illuminate the specimen.a. 5pecimens must be prepared for viewing in the electronmicroscope. 5uch preparation includes fixation free9e(etchingand thin sectioning.

b. The scanning electron microscope sees surface details in athree(dimensional image. c. The scanning tunneling microscope also views surfacestructures of specimens but its resolving power is much greaterthan the electron microscope. Individual atoms can be seen.

II Micro!co)$ T$c*ni3u$!1 St ining



+. 5imple staining procedures involve a single dye,. ositive stains color cell components whereas negative stains do not

penetrate the cell.#. /ifferential staining techni!ues make use of a combination of dyes.

1. The pram stain divides bacteria into two groups based upon theircell wall composition& Erampositive and Eram(negative.

2. The acid(fast stain is used on members of the genusMycobacterium which cause tuberculosis and leprosy.

". 5pecific cell structures can be stained by using special techni!uesthat depend on the structure of the material being stained.

III. S* )$! o- B ct$ri+. ,acteria have three ma%or shapes& cylindrical or bacillus> spherical orcoccus> and spiral or spirillum.,. Individual cells especially cocci may remain attached to one anotherforming particular arrangements that are useful in identifying genera.I+. ,unction! R$3uir$d in Pro4 r'otic nd Eu4 r'otic C$%%!+. +ll cells must carry out the following functions&

1. =nclose the internal contents of cell>2. replicate genetic information>". synthesi9e cellular components> and$. generate store and utili9e energy(rich compounds.

,. In addition some cells can move transfer genetic information store

reserve materials and form a new cell type the endospore.+. Enc%o!ur$ o- C'to)% !" in B ct$ri+. The cytoplasm is enclosed by three layers& the capsule cell wall andcytoplasmic membrane.,. #apsule or slime layer 1. 5ome cells synthesi9e a capsule or slime layer when growingunder certain nutritional conditions. Mostcapsules are composed of polysaccharides. They are protective to the celland help attach bacteria to a variety of surfaces.

#. #ell wall1. The bacterial cell wall has several important functions for the cell

and its composition confers important properties on it. The cell wall holds acell together and gives the cell its shape.

2. The uni!ue structure in all bacterial cell walls that confers rigidityis glycan which consists of repeating subunits of M(acetylglucosamine

%oined to N(acetylmuramic acid %oined to other glycan layers by amino acid bridges. =ach layer is termed a peptidoglycan layer.

". #ell walls of Eram(positive bacteria consist of multiple layers of

peptidoglycan whereas cell walls of Eram(negative bacteria consist of a



single layer of peptidoglycan with several other additional layers. Theseinclude lipoprotein lipopolysaccharide and phospholipid.

$. +rchaebacteria have no peptidoglycan in their cell walls.). /ifferences in cell wall composition account for the Eram(staining

properties and the effectiveness of penicillin./. #ytoplasmic membrane+ll cells both prokaryotic and eukaryotic have a cytoplasmic membranethat determines which molecules enter and leave the cell.

1. #hemical composition. The cytoplasmic membrane is composed of lipoprotein and phospholipids.

2. 5tructure8the cytoplasmic membrane is a bilayer membrane.". @unctions8in bacteria the cytoplasmic membrane is the site of

en9ymes of energy generation> it controls the exit and entrance ofmolecules by the mechanisms of diffusion and active transport.

$. In eukaryotic cells it forms a series of membranes called theendoplasmic reticulum. 6ther internal membranes surround structuressuch as lysosomes and the Eolgi apparatus.

+I. G$n$r tion o- En$rg' in Eu4 r'otic C$%%!+. =nergy is generated by mitochondria and chloroplasts. ,oth organellesoriginated from bacteria that were engulfed by a primitive eukaryotic cell.

+II. C$%% Mo#$"$nt

+. The ma%or structures responsible for movement in all cells are flagella.,. @lagella have a relatively simple structure in bacteria. They consist ofthree parts& filament hook and basal body.#. @lagella push bacteria which swim through li!uids.

1. ,acteria move toward food sources and away from harmfulmaterials the process of chemotaxis. 2. #hemotaxis is a primitive nervous response and operates bydetermining the length of time the bacteria swim in one direction./. In eukaryotic cells the structure of flagella in eukaryotic cells is more

complex than in bacteria. @lagella move in a whiplike motion to push or pullthe cells.+III. C$%% Att c*"$nt+. ili are protein appendages of attachment.I/. Stor g$ o- G$n$tic In-or" tion+. The ma%or structure in which the genetic information of all cells is storedis the chromosome.,. The bacterial chromosome is a long double(stranded circular /N+molecule.



1. In prokaryotic cells only one or several chromosomes are present per cell and it is not surrounded by a nuclear membrane.

2. ,asic proteins are bound to the /N+.#. lasmids are small /N+ molecules that code for nonessentialinformation and replicate independently of the chromosome./. In eukaryotic cells genetic information is contained in numerouschromosomes each of which carries different information.

1. =ach /N+ strand is composed of double(stranded /N+ woundaround basic proteins making up a structure called chromatin.

2. The nucleus also contains the nucleolus which plays a role insynthesis of ribosomes.

/. S'nt*$!i! o- Prot$in+. ;ibosomes are structures on which proteins are synthesi9ed.

1. ;ibosomes are composed of ribosomal protein and ribosomal;N+.

2. =ukaryotic ribosomes differ from prokaryotic ribosomes in thatthey contain different proteins and ;N+ and also differ in weight.,. Many antibiotics inhibit the correct functioning of prokaryotic ribosomeswithout affecting eukaryotic ribosomes./I. Stor g$ M t$ri %!+. ,acteria often store a variety of materials that they later use as a sourceof nutrients. These include glycogen volutin and ,(hydroxybutyric acid./II. Endo!)or$!+. The endospore is a uni!ue cell type that develops from activelymultiplying cells :vegetative cells< when they face starvation.,. =ndospores have unusual staining and resistance properties.#. Many endospore(producing bacteria cause disease.

DYNAMICS O, BACTERIAL GROWTHThis chapter describes how microorganisms grow. Microorganisms

are under the influence of the same factors that control the growth of anyother organism. 7owever microorganisms do have some uni!ue features intheir growth patterns and their small si9e presents certain problems inmeasuring their growth. ,acteria multiply by binary fission in which onecell produces two identical daughter cells. Bhen we describe the growth of

bacteria we talk of the growth of populations rather than of individuals. Thischapters explores the factors that affect the growth of mircoorganisms anddescribes how these factors often determine the habitat in which anorganism grows.

KEY CONCEPTS



1. ,acterial growth is measured by an increase in cell numbers> growth ofmost other organisms is measured by an increase in their si9e.

2. +ll bacteria re!uire a source of carbon to synthesi9e components ofcytoplasm as well as a source of energy in order to grow. /ifferent

bacteria use different materials for their nutrients.". The growth re!uirements of bacteria may change permanently when they

are taken from their natural environment and are grown in the laboratory.$. ;epresentatives of different groups of bacteria can multiply over a very

broad range of environmental and nutritional conditions.). ,acteria are often able to alter their internal environment to compensate

for changes in the external environment.SUMMARY

I. Pur$ Cu%tur$ M$t*od!+. In nature bacteria exist as a mixed population.,. #olonies represent the offspring of a single cell and the streak platemethod is used to separate cells.#. The properties of agar make it ideal for growing bacteria on a solidsurfaceII. M$ !ur$"$nt o- C$%% Gro t*+. ,acterial growth is defined in terms of population si9e not by si9e of individual cells.

1. ,acteria divide by binary fission.

2. Number of bacteria increases exponentially.,. There are several methods for measuring bacterial growth.

1. 5cattering of light measures living and dead cells.2. Erowth can be measured as an increase in cell number.

a. late count measures number of viable cells that can grow into acolony. b /irect microscopic count is rapid but does not distinguish

between living and dead bacteria.III. Mu%ti)%ic tion o- Microorg ni!"!(G$n$r % A!)$ct!

+. Microorganisms multiply under an enormous range of environmentalconditions,. +n organism taken from its natural habitat often shows altered growthre!uirements when grown in the laboratory.I+. , ctor! In-%u$ncing Micro&i % Gro t*+. =nvironmental factors that influence growth include temperatureoxygen p7 and osmotic pressure.

1. Temperature of growth. Most bacteria grow within a temperaturerange of approximately " F#.

a. sychrophiles(optimum growth temperature is between ()F and 2 F#.



b. Mesophiles8optimum growth temperature is between 2 F and ) F#.c. Thermophiles(optimum growth temperature is between ) F and 0 F#.d. =xtreme thermophiles(optimum growth temperature is above 0 F#.

2. 6xygen re!uirements for growth.a. 6bligate :strict< aerobes have an absolute re!uirement for oxygen.

b. 6bligate :strict< anaerobes cannot multiply if oxygen is presentsince it kills bacteria.c. @acultative anaerobes can utili9e oxygen if it is available but cangrow although less well in its absence.d. Microaerophilic organisms re!uire small amounts of oxygen:2A(1 A< but higher concentrations are toxic.e. +erotolerant organisms grow in the presence or absence ofoxygen but they derive no benefit from the oxygen.

". +erobes re!uire oxygen because they have metabolic pathwaysthat re!uire oxygen to convert energy in foodstuffs into forms useful tothe cell.

a. ,acteria that re!uire oxygen have the means to detoxify toxicforms of oxygen such as hydrogen peroxide.

b. /etoxifying en9ymes include catalase and superoxide dismutase. $. Most bacteria grow best in a medium with a p7 :neutral<.

a. ,uffers are added to media to maintain a constant p7.

b. ,acteria can maintain their internal contents at neutral p7 even thoughthe external p7 is below or above this.

). 6smotic pressure is determined by the concentration of dissolvedsubstances in the medium in which bacteria are growing.

a. Gnder normal conditions the osmotic pressure is slightly higher on the inside than on the outside of the cell.

b. ,acteria can compensate for pressure differences to a certainextent if the external osmotic pressure is high.+. Nutrition % A!)$ct! o- B ct$ri % Gro t*

+. #ell multiplication re!uires a source of energy and raw materials for synthesis of cell components.

1. 5pectrum of nutritional types&a. hotoautotrophs use light :radiant< energy and #6H as a sourceof carbon.

b. hotoheterotrophs use light :radiant< energy and organiccompounds as a source of carbon.c. #hemoautotrophs use chemical energy and #6H as a source ofcarbon.

d. #hemoheterotrophs use chemical energy and organic compounds



as a source of carbon.e. -ithoheterotrophs use an inorganic source of energy and organiccompounds as a source of carbon.

2. +ll organisms re!uire a supply of nitrogen sulfur and phosphorous.". Erowth factors&

a. ,acteria re!uire small molecules that serve as subunits of biosynthetic macromolecules and cell components.

b. 5ome bacteria can synthesi9e all of their growth factors> othersthat lack the necessary biosynthetic en9ymes must have them

provided.+I. Cu%ti# tion o- B ct$ri in t*$ L &or tor'+. The two kinds of media on which bacteria are grown are synthetic:defined< or complex :undefined< media.

1. 5ynthetic medium consists of chemically pure materials added inknown amounts.

2. #omplex :undefined< medium consists of undefined nutrients suchas ground meat added in known amounts.

+II. Pro&%$"! A!!oci t$d it* Gro t* o- Microorg ni!"! in t*$L &or tor'+. No single medium has been devised on which all bacteria will grow.

This may result from several factors&

1. Toxic compounds may be present and must be removed.2. Gnusual growth factors may be needed.

". 5ome bacteria can only be grown in mixed culture similar to theirnatural environment.6ne bacterium provides what the other oneneeds.

,. +naerobes re!uire special cultivation methods.1. +n anaerobe %ar may be used to remove all oxygen.2. #hemicals may be added to react with the oxygen.

+III5 Cu%ti# tion o- Org ni!"! t* t Occur ! Minor P rt o- t*$

Micro&i % Po)u% tion+. =nrichment cultures enhance the growth of specific organisms.,. 5elective media preferentially inhibit the growth of certain organisms.I/. D'n "ic! o- B ct$ri % Po)u% tion Gro t*(,our W$%%6r$cogni7$d

P* !$!+. -ag phase of growth involves no increase in cell numbers8the 'tooling(up' phase.,. =xponential phase of growth is the time during which cell number increases exponentially.



#. 5tationary phase is reached when the numbers of viable cells stopsincreasing./. /eath phase is characteri9ed by an exponential decrease in the number of viable cells./. Gro t* o- B ct$ri % Co%on'+. #olony enlargement results from cells multiplying at the outside edges of the colony./I. Gro t* o- B ct$ri in N tur$+ In the laboratory bacteria grow in a closed system> nutrients are notrenewed and waste products are not removed.,. +n open system is the typical system found in nature. Nutrients arereplenished and waste products are removed.

1. + chemostat in the laboratory simulates an open system innature.

2. The doubling time as well as the population si9e of bacteria can be controlled by a chemostat.

8. METABOLISM1 THE GENERATION O,ENERGY AND SYNTHESIS O, SMALL

MOLECULES

+s an essential function of life organisms take in nutrient molecules>degrade them to generate energy and smaller molecules> then using theenergy they reassemble these small molecules to meet their own needs. Thisvery basic process of life is known as metabolism. This chapter focuses onthe catabolic portion of metabolism during which nutrient molecules are

broken down to generate energy and small molecules. These products of catabolism are then available for reassembly. ;espiration and fermentationare the processes by which the cell accomplishes both the generation of energy and of small molecules. Many of these small molecules can be used

for identification of bacterial species. The chapter ends with a look at someother ways in which microorganisms generate energy.

KEY CONCEPTS1. #ells must carry out two metabolic functions& 1< degrade foodstuffs to

generate energy and small molecules and 2< use the energy to convertthe small molecules into marcomolecules and cell structures.

2. @oodstuffs are degraded by two ma%or pathways& respiration or fermentation.

". ;espiration produces much more energy than fermentation for the same

amount of foodstuff degraded.



$. The tricarboxylic acid cycle has two functions& 1< to produce energy and2< to synthesi9e compounds that are converted into amino acids.

). ,acteria as a group have a wide variety of en9ymes and synthesi9e a largenumber of different products. Identifying these end products can helpidentify the different species of bacteria.

SUMMARYI. O#$r#i$+. To multiply cells must degrade :cataboli9e< foodstuffs to gain energy.

@oodstuffs also serve as a source of precursor metabolites for thesynthesis of subunits of macromolecules. The synthesis of cellcomponents :anabolism< re!uires energy.

II. En7'"$!(C*$"ic % Kin$tic! nd M$c* ni!" o- Action+. =n9ymes rearrange atoms under the mild conditions of temperature and

pressure at which cells can live.,. =n9ymes speed up reactions by lowering their activation energy.#. The shape of the substrate must fit the shape of the en9yme that acts on it.

1. +n en9yme functions by combining with its substrate through weak bonding forces. Next the products

of the reaction are released leaving the en9ymes unchanged./. =nvironmental and chemical factors influence en9yme activity.

1. Important features of the environment include temperature p7and salt concentration.

a. + 1 F# rise in temperature doubles the speed of en9ymaticreactions.

b. Most en9ymes function best near a p7 of .2. =n9ymes are inhibited by a variety of compounds that may result in a

reversible or irreversible inhibition. +n example of reversible inhibition is sulfadrugs which compete with para(aminoben9oic acid for the active site of anen9yme used to synthesi9e the vitamin folic acid. +n irreversible inhibitor mayalter amino acids that give the en9yme its shape.

III. En$rg' M$t &o%i!"

+. 6ne of the pathways of energy metabolism involves the en9ymaticconversion of a large number of lowenergy bonds to a few high(energy

bonds from which +T the storage form of energy can be synthesi9ed.,. The two ma%or pathways for generating energy are fermentation in whichan organic compound is the final hydrogen acceptor and respiration inwhich an inorganic compound is the final hydrogen acceptor.#. ,oth pathways also generate precursor metabolites for the synthesis ofcell components. ;espiration but not fermentation produces reducing

power.

/. Elycolysis is the most common pathway for degrading sugars.



1. + glucose molecule metaboli9ed through the glycolytic pathwayresults in the production of 2 molecules of +T 2 molecules of pyruvicacid and 2 molecules of N+/7.

2. The pyruvic acid is metaboli9ed to different compounds dependingon the species of bacterium and whether or not oxygen is present :a< Ifoxygen is not present pyruvate is converted to a variety of productsusing the N+/7 generated in glycolysis. These include& :1< lactic acidin lactic acid fermentation :2< alcohol and #6H in the alcoholicfermentation and :"< a variety of other compounds in a mixedfermentation.

I+. En$rg' M$t &o%i!"(R$!)ir tion+. The T#+ cycle oxidi9es pyruvic acid to #6H and 7H6 and then traps theenergy of pyruvic acid in +T .

1 #arbon skeleton transformation8The acetyl #o+ is converted to 2molecules of citric acid which is converted to 2 molecules of #6y and $

N+/7 molecules in every turn of the T#+ cycle. 2. =nergy transformations8The electrons for the hydrogen atomsremoved in the reactions are transferred through the electron transport chainwhich generates the high(energy bonds of +T . This process is calledoxidative phosphorylation.,. Much more energy is gained in respiration than in fermentation.

1. +bout 2 times more energy is gained if glucose is oxidi9ed

completely to #6 2 and 7 26 rather than if its metabolism stops at pyruvic acid.

+. R$!)ir tion Und$r An $ro&ic Condition!+. 5ome bacteria can utili9e other inorganic compounds besides oxygen aselectron acceptors. The most common acceptors are nitrate sulfate andcarbon dioxide. -ess +T is generated compared to aerobic respiration.+I. M$t &o%i!" o- Co")ound! Ot*$r t* n G%uco!$+. 5ome bacteria have pathways other than the glycolytic pathway.+II. Ot*$r P t* '! o- G%uco!$ D$gr d tion

+. =ntner(/oudoroff athway,. entose(phosphate pathway provides reducing power for biosynthesis aswell as certain precursor metabolites.+III. O9id tion o- Inorg nic Co")ound!+. 5ome bacteria can oxidi9e a variety of inorganic compounds to gainenergy.I/. Bio!'nt*$tic M$t &o%i!"+. /egradative and biosynthetic pathways may be part of the same pathway.

1. /egradative pathways generate the compounds that serve as

starting materials for the synthesis of cell components.



,. Many amino acids are synthesi9ed from the same precursor metabolites.#. + very important reaction in biosynthetic metabolism is the mechanism

by which N7H is incorporated into organic compounds. +n especiallyimportant reaction is the addition of N7 to a(ketoglutaric acid to formglutamic acid. This reaction is reversible and connects anabolism withcatabolism. The N7H can be transferred to a variety of other a(keta acids toform other amino acids./. urines and pyrimidines are synthesi9ed stepwise along different

pathways./. B ct$ri % P*oto!'nt*$!i!+. -ight energy absorbed by chlorophyll provides energy to reduce #6H tocell material.,. #ompounds other than I-6 serve as the reducing agent in photosynthetic

bacteria other than cyanobacteria. 1. If oxygen is released then photosynthesis is termed oxygenic> if itis not released it is termed anoxygenic.#. hotosynthesis re!uires light for energy generation but biosyntheticreactions do not.

1. '-ight' reactions only occur in photosynthetic organisms that gainenergy from light. =lectrons aretransferred along an electron transport chain and +T is generated in the

process.

2. '/ark' reactions. +ctually formation of carbohydrate can occur inlight or dark. + key reaction is the addition of #6H to the )(carboncompound ribulose 1 )(biphosphate to form a metabolite in theglycolytic pathway. This compound is converted to cell components.

:. IN,ORMATIONAL MOLECULES1 ,UNCTION5 SYNTHESIS5

AND REGULATION O, ACTI+ITY

In order to reproduce and to carry on the many activities associatedwith life cells must have a plan or blueprint to follow. These instructions arecarried in the form of a macromolecule called /N+. /N+ is an ama9ingmolecule not only because it contains the codes for every life function butalso because it reproduces itself and rarely makes a mistake. In addition toreplication /N+ also directs the synthesis of another macromolecule ;N+that serves as a messenger in the process of protein synthesis. The code for

the life is actually a code for the synthesis of proteins. #ells monitor their



environment and synthesi9e only those proteins that are necessary at that particular moment. #ells have a means of control or regulation of their protein synthesis.

KEY CONCEPTS1. The general rule for the flow of information in cells is& codes for codes for/N+8 ;N+8 rotein the synthesis of amino acids in2. In the transfer of information a se!uence of nucleotides in /N+

determines a se!uence of amino acids in proteins.". /N+ has two functions& to store genetic information and to reproduce

itself.$. The se!uence of nucleotides in one strand of /N+ determines the

se!uence in the other strand.). The en9ymes of bacteria may change with changes in the environment

because it turns on and turns off gene functions.*. The synthesis of many small molecules such as amino acids is controlled

by regulating the activity as well as the number of en9yme moleculesinvolved in the synthesis of the amino acid.

. ,acteria synthesi9e only the amounts of each cell component that theyneed in order to multiply most rapidly.

SUMMARY

I. C*$"i!tr' o- DNA nd RNA+. /N+ occurs as a double(stranded helix held together by hydrogen bonds

between adenine and thymine and between guanine and cytosine.,. The two strands run in opposite direction one going form the top to the

bottom> the other from the bottom to the top.#. ;N+ is usually single(stranded and shorter than /N+.II. In-or" tion Stor g$ nd Tr n!-$r+. Information is stored in /N+ and ;N+ in the se!uence of their nucleotide subunits.

,. Information in /N+ can be transferred by two different processes.1. The se!uence of nucleotides in /N+ can be transferred to m;N+

which determines the se!uence of amino acids in proteins.2. ;eplication of /N+8This begins at a specific site on the

chromosome and proceeds by the se!uential addition of nucleotides by/N+ polymerase. Two chromosomes identical to the original areformed.

III. E9)r$!!ion o- G$n$!



+. + bacterial chromosome consists of two ma%or regions. 6ne codes for proteins :coding region<> the other determines whether the first region will be expressed :regulatory region<.,. The se!uence of three nucleotides in m;N+ determines a specific aminoacid a triplet code.#. Eene transcription is the process of making an ;N+ copy of the geneticinformation in /N+. 1. There are three steps in transcription. a. Initiation8The sigma factor of ;N+ polymerase bind to a

promoter region in the regulatory region of the gene. b. =longation8;N+ polymerase moves along one of the strands of /N+ :template strand< synthesi9ing a complementary single strandof m;N+.c. Termination8;N+ polymerase comes to a stop signal at the end

of a gene and is released./. The second step in gene expression is the translation of m;N+ into

protein.1. The sets of three nucleotides :codons< that code for each amino

acid have been identified. Most amino acids have several codons.2. Translation involves three steps.

a. Initiation8The ribosome binds to a region near the beginning of them;N+ to start translation.

b. =longation8+ charged t;N+ molecules attach to its complementarycodon of the m;N+ positioned at a particular site on the ribosome. The ribosomemoves along the m;N+ three nucleotides at a time so that another charged t;N+

bonds to the next complementary codon. The amino acids are %oined together in a peptide bond. c. Termination8Bhen the ribosome reaches a stop codon in them;N+ the protein dissociates from thet;N+ and protein synthesis stops.I+. Di--$r$nc$! B$t $$n Pro4 r'otic nd Eu4 r'otic G$n$

Tr n!cri)tion;Tr n!% tion+. There are a number of differences.

1. In prokaryotic cells transcription and translation occur almostsimultaneously> in eukaryotes m;N+ is transported out of the nucleus

before translation begins. 2. In eukaryotes most m;N+ molecules are modified before they are

translated. ,locks of nucleotidesare cut out a situation very rare in prokaryotes.

+. T*$ En#iron"$nt nd Contro% S'!t$"!



+. ,acteria may be sub%ected to rapidly changing nutrients in theenvironment. They have the means to shut off or activate pathways of

biosynthesis and degradation so as to synthesi9e only the materials theyneed in any particular environment.

+I. M$c* ni!"! o- Contro% o- Bio!'nt*$tic P t* '!+. =nd product repression controls the start of gene transcription.

1. The end product binds to the represser and changes its shape sothat it can then bind to the operator region of the gene. This prevents the ;N+ from binding to the promoter.,. =nd products control the activity of the first en9yme of the biosynthetic

pathway :allosteric control<.1. The end product combines with the first en9yme of the pathway

and changes its shape so that it can no longer cataly9e its reaction. Theinhibition of the first en9yme shuts down the entire pathway.+II. M$c* ni!"! o- Contro% o- D$gr d ti#$ P t* '! +. Metabolites that can be degraded activate the genes responsible for their

degradation.1. The compound to be degraded turns on the pathway that degrade it.

The compound binds to the represser protein and activates it therebyallowing the ;N+ polymerase to initiate transcription.,. #atabolite repression ensures efficient use of available foodstuffs.

1. + catabolite represser can reduce the level of cyclic +M re!uired

for induction of certain pathways so the catabolite represser ismetaboli9ed first.

#. 5ome very important en9ymes are synthesi9ed at the same levelindependent of the medium. These are termed constitutive.

BACTERIAL GENETICS,acterial genetics is probably the fastest growing area of

microbiology today. =lucidation of the chemical structure of/N+ has

!uickly led to an understanding of how cells function at a molecular level.This chapter describes the structure of/N+ as well as how changes in thatstructure produces mutations. These mutations are spontaneous but canincrease in fre!uency in the presence of mutagens. ,acteria are notconsidered sexually reproducing organisms but there are processes bywhich some bacteria can undergo genetic recombination. These processesare used to better understand the genetics of bacteria.

KEY CONCEPTS1. +ntibiotics and other harmful agents in the environment do not cause

mutations but rather select for pre(existing mutations in the population.



2. In bacteria small pieces of the chromosome can be transferred from onecell to another.

". Eenes can move from one location in /N+ to other locations in the /N+of the same cell.

$. lasmids confer a large number of different but dispensable properties on bacteria and are readily transferred to other bacteria often unrelated toeach other.

). ,acteria are able to protect themselves from foreign /N+ entering thecell.

SUMMARYI. Sourc$ o- Di#$r!it' in Microorg ni!"!+. Two ma%or sources account for diversity. 1. ?ariation in se!uences of nucleotides that exist in /N+. 2. The environment regulates gene function and en9yme activity.II. A%t$r tion! in Nuc%$otid$ S$3u$nc$ in DNA+. Mutations can occur by substitution of one nucleotide for another.,. Mutations can occur by the removal or addition of nucleotides.#. Mutagens increase the fre!uency of mutations.III. Mut g$n$!i! I! t*$ Proc$!! &' W*ic* Mut tion I! Produc$d+. 5pontaneous mutations occur in the absence of any known mutagen.These mutations are however the same types as those caused by mutagens.,. Three types of mutagens are known. These are chemical agents

transposable elements and radiation.#. #hemical mutagens often act by altering the hydrogen(bonding propertiesof the bases.

1. #hemical mutagens include alkylating agents base analogs andintercalculating agents.

2. ,ase analogs are incorporated into /N+ in place of the natural base.

". Intercalating agents result in the addition of nucleotides.I+. Tr n!)o! &%$ E%$"$nt!

+. Transposable elements are segments of /N+ that move from one site in a/N+ molecule to another. They insert into genes and disrupt their function.,. Insertion se!uence is the simplest transposable element. It is composed of two inverted se!uences flanking an en9yme re!uired for transposition.#. More complex transposable elements code for antibiotic resistance.+. U%tr #io%$t Irr di tion(U%tr #io%$t Lig*t nd / R '! Ar$ Mut g$nic+. Gltraviolet light causes formation of thymine dimers.+I. R$) ir o- D " g$d DNA+. G? damage can be overcome by an inducible en9yme system of /N+

replication that bypasses the damaged /N+ but makes many mistakes. This



is the 565 system.,. ?isible light activates an en9yme that breaks covalent bonds formingthymine dimers the process called light repair.#. ,acteria can excise damaged /N+ and replace it with undamaged /N+which is called excision repair or dark repair.+II. R t$! o- Mut tion+. Eenes mutate independently of one another and mutations are stable.,. Mutations are expressed rapidly in prokaryotic cells because they haveonly one or two identicalchromosomes.+III. Mut nt S$%$ction+. /irect 5election re!uires that the mutant grow on a solid medium onwhich the parent cannot.,. Indirect selection must be used to isolate mutants that cannot grow on amedium on which the parent can grow.

1. ;eplica plating involves transferring all of the colonies on one plate to another plate simultaneously.

2. enicillin enrichment increases the proportion of mutants in a population. It is based on the fact that penicillin kills growing cells only.

I/. Condition % L$t* % Mut nt!+. #onditional lethal mutants result from mutations in genes that would

ordinarily be lethal.,. These conditional lethal mutations are usually in genes that are involvedin macromolecular synthesis./. C*$"ic %! c n &$ t$!t$d -or t*$ir c nc$r6c u!ing &i%it' &' t*$ir

"ut g$nic cti#it'. T*$ A"$! t$!t "$ !ur$! t*$ -r$3u$nc' o-r$#$r!ion o- *i! to *i!< c$%%!.

/I. M$c* ni!" o- G$n$ Tr n!-$r(G$n$r % A!)$ct!+. Eenes can be transferred between bacteria by three different mechanisms.,. 6nly short segments of /N+ are transferred.

#. ;ecombination between donor and recipient /N+ occurs by breakageand reunion mechanism. 1. /N+(mediated transformation involves the transfer of naked

/N+. ;ecipient cells must be able totake up /N+ through their envelope8natural competence. #ells thatcan have holes punched in their envelopes with an electric current8 artificial competence.

2. Transduction involves viral transfer of /N+.". #on%ugation re!uires cell(to(cell contact. Gsually only plasmids are

transferred from @1

4 to @ cells.



7fr cells are formed if the @J plasmid integrates into the chromosome.7fr cells can transfer chromosomal /N+. @4 donor cells result when the @J plasmidintegrated into the chromosome isexcised and carries a piece of chromosomal /N+ with the plasmid.

/II. P% !"id!+. ;(factor plasmids confer resistance to a large number of antimicrobialagents. They can be transferred often to related and unrelated bacteria bycon%ugation./III. G$n$ Tr n!-$r Wit*in t*$ S "$ B ct$riu"+. Transposable elements are important for the transfer of genes to unrelated

bacteria because they can move from a chromosomal site to a plasmidwhich can then be transferred by con%ugation./I+. R$!triction nd Modi-ic tion o- DNA+. /N+ entering unrelated bacteria is recogni9ed as being foreign and isdegraded by deoxyribonucleases termed restriction en9ymes which cleavethe /N+ at restricted or specific sites.,. Modification en9ymes confer resistance to restriction by altering thenucleotides in the /N+ at the sites where the restriction en9ymes cleave the/N+./+. I")ort nc$ o- G$n$ Tr n!-$r to B ct$ri+. Eene transfer allows microorganisms to survive changing environments

by providing recipient cells with whole new sets of genes./+I. I")ort nc$ o- G$n$ Tr n!-$r to t*$ Micro&i % G$n$tici!t+. Eene mapping8Eenes that are close together will be transferred together

by con%ugation transformation and transduction. +nalysis of these transfersallows for the calculation of relative distances between genes.,. Eenetic =ngineering8Eene transfer is the method that genetic engineersuse to introduce /N+ into bacteria.

=. MICROBIOLOGY AND BIOTECHNOLOGY

Terms such as gene cloning recombinant /N+ and geneticengineering are becoming commonplace in our language and our lives.7ardly a week goes by without one of these terms appearing in a newsmaga9ine or on the evening news broadcast.This chapter introduces you to the application of microbial genetics to areasof biotechnology. The methods of gene cloning genetic engineering and the

polymerase chain reaction which did not exist 2 years ago are explored



with examples of how these new technologies are important in today4ssociety.

KEY CONCEPTS1. /N+ is a macromolecule that is easily studied and manipulated in a test

tube.2. The discovery of restriction en9ymes opened the door to gene cloning and

genetic engineering.". In the laboratory /N+ from one organism can be introduced to other

organisms where it will replicate and be expressed.$. Eene cloning can provide large amounts of specific /N+ for study as

well as large !uantities of products coded by the cloned /N+.). The polymerase chain reaction technology is probably the most important

technical advances made in molecular biology in the past decade.SUMMARY

I. R$co"&in nt DNA T$c*no%og' In#o%#$! S$ri$! o- T$c*ni3u$! t* tIn#o%#$ t*$ M ni)u% tion o- DNA Mo%$cu%$ Out!id$ C$%% ndR$!u%t! in t*$ ,or" tion o- N$ DNA Mo%$cu%$!. T o T$c*ni3u$!

r$ o- S)$ci % I")ort nc$.+. Eene cloning8propagating /N+ of a particular cell in a new hostcell.,. Eenetic engineering8modifying the properties of cells byintroducing recombinant /N+ molecules that express their genes.

II. B !ic ,$ tur$! o- G$n$tic Engin$$ring+. Techni!ues are fundamentally the same as natural processes occurring incells to produce recombinant /N+ molecules but /N+ may come fromunrelated organisms.,. + common method of gene cloning involves the 'shotgun' techni!ue inwhich all of the genes of an organism are cloned and the gene of interest isthen identified.#. The ma%or steps in shotgun cloning are&

1. ;elease of /N+ from the host cell.

2. #onstruction of recombinant /N+ molecules. This involvesrestriction endonucleases and %oining/N+ to a plasmid.

". Introduction of recombinant /N+ molecules into host organism:usually =. coil< by /N+transformation.

$. 5election of host cells that contain recombinant /N+8usually byinoculating on antibiotic(containing medium.

). Identification of cells carrying the desired recombinant /N+ clone

usually done by hybridi9ation to a known /N+ probe.



III. E9)r$!!ion o- C%on$d G$n$!+. Eene expression re!uires that the host cell recogni9e the promoterribosome binding site and stop signals for transcription and translation.These signals for expression can be cloned onto genes.,. The more closely related two organisms are the more likely the genes of one will be expressed in the other.I+. A))%ic tion o- G$n$tic Engin$$ring in Biot$c*no%og'+. Microorganisms can be manipulated to give them new properties.

1. Increasing the number of copies of a gene cloned on a multicopynumber plasmid can increase the !uantity of the protein coded bythe gene.

,. #linically important proteins can be produced in =. coli and yeast. 5uch products include insulin human growth hormone blood clotting factorsinterferons and several different vaccines.+ Addition % A))%ic tion! o- Biot$c*no%og'+. ,ioremediation involves the use of microorganisms to degrade harmfulchemicals.

1. @ertili9ers have been applied to oil soaked beaches in +laska toencourage the growth of existing

microorganisms that then could break down the oil., Toxins from bacteria can serve as effective biocontrol agents for insects.

1. The natural insecticides from ,. thurmgiensis :,. T. toxin< can be

cloned into cells of seudomonas which are killed and then appliedto plants.2. The ,. T. toxin gene can be cloned into a variety of plants which

then become resistant to insect pests.# In plant genetic engineering genes are introduced into the plants by+grobacterium.

1. To get bacterial genes expressed in plants it is necessary to use a plant promoter and ribosome binding site as well as plant stop signals for gene expression.

+I. Biot$c*no%og' nd t*$ Po%'"$r !$ C* in R$ ction >PCR?+ olymerase chain reaction allows researchers to duplicate specific piecesof /N+ one billionfold in an hour.,. #; involves the denaturation of /N+ annealing of two primers toeither end of the /N+ to be copied and then synthesi9ing two strands fromthe primer each complementary to one of the original strands. The cycle isthen repeated.#. Microorganisms that cannot be cultured can still be identified using acombination of #; technology /N+ se!uencing and probe technology.



@. CONTROL O, MICROBIAL GROWTH

The control of microbial growth is essential not only for healthreasons but also for the preservation of the foods we eat the clothes wewear even the preservation of the homes where we live. 5ome methods of control such as the preservation of food by drying or salting are as old ascivili9ation. Most methods of control are directed towards the most difficultforms of bacteria to kill the endospores. + number of chemical or physicalagents are available but heat is probably the most common application. It isessential to understand the difference between an agent that is bacteriostaticand one that is bactericidal. @ailure to understand this could have veryserious conse!uences.

KEY CONCEPTS1. 5terili9ation is the process of removing or killing microorganisms and

viruses in or on a material. /isinfection in contrast implies only areduction in the number of infectious agents to a point where they nolonger present a ha9ard.

2. Time temperature growth stage of the organism nature of thesuspending medium and the numbers of organisms present must all beconsidered when determining which sterili9ation or disinfectiontechni!ue to employ.

". 5terili9ation and disinfection can be accomplished by using heatfiltration chemicals or radiation.

$. /eath of infectious agents generally occurs loganthmically.SUMMARY

I. A))ro c*$! to Contro%+. 5terili9ation is the process of killing or removing all microorganisms andviruses in or on a material.,. /isinfection reduces the number of pathogens but does not necessarilyeliminate all living agents.

II. Princi)%$! In#o%#$d in Ki%%ing Microorg ni!"!+. /uring sterili9ation only a fraction of the microorganisms or viruses dieduring a given time interval.,. The time to achieve sterility depends partly on the number of organisms

present at the beginning of sterili9ation#. /ifferent microorganisms and viruses vary in their susceptibility tosterili9ing and disinfecting procedures./. Numerous conditions alter the effectiveness of agents that kill

microorganisms and viruses.



III. Ki%%ing Microorg ni!"! nd +iru!$! &' U!ing H$ t+. 7eat kills by coagulating the proteins of cells and viruses.,. The use of heat is limited to substances that can withstand temperaturesre!uired for microbial killing.#. /ry heat re!uires more time than wet heat to kill microorganisms.,oiling kills vegetative cells and viruses but is not reliable for killingendospores./. ressure cookers and autoclaves are effective sterili9ers if properly used.=. asteuri9ation involves controlled heating at temperatures below boiling.It is not a sterili9ing procedure but eliminates many potential pathogens anddelays spoilage.I+. St$ri%i7 tion &' ,i%tr tion+. The effectiveness of filters depends on multiple factors such as pore si9echemical nature of the suspending fluid and the amount of pressure totransfer fluid across the filter.,. 5ome membrane filters have such a small pore si9e that they are able tofilter viruses from a suspension.+. C*$"ic % Di!in-$ct nt!+. #hemical disinfectants are generally less effective in the presence of organic materials.,. 7eat enhances their chemical action against microorganisms and viruses.#. #hemical disinfectants work slowly against bacterial endospores

Mycobacterium tuberculosis and certain small nonenveloped viruses/. + disinfectant is chosen on the basis of its chemistry :phenolic halogen!uaternary etc.< the conditions under which it will be used :for example arubber material would not tolerate household bleach> !uaternary ammoniumcompounds would be inactivated by pus or gau9e< and how strict is theneed for sterility.=. +lcohols are not effective against spores.@. 7alogens include chlorine and iodine compounds lodophores releaseiodine but are unreliable under certain conditions.

E. @ormaldehyde has limited use because it is slow to act againstendospores and some viruses the vapors are irritating and it is a carcinogen.7. henolics include cresols and xylenols.

1. In high concentrations most phenolics kill Mycobacteriumtuberculosis.

2. 5ome lack antiviral activity.". Ma%or advantages are wide spectrum of activity reasonable cost

and ability of some to remain active in the presence soaps and otherorganic material.



$. 7exachlorophene effectively prevents staphylococcal infections but it has little activity against many Eram(negative bacteria andabsorption through the skin and through wounds is a potential ha9ard.

I. Kuaternary ammonium compounds are surface active substances that areeffective saniti9ing agents. Gses& disinfection of clean inanimate ob%ects

preservatives in non(food materials such as eye medicines. They have thedisadvantage of being easily inactivated by soaps and other organic materialincluding gau9e.L. The use of metal compounds has decreased because of their generally

bacteriostatic activity inability to kill spores and their contribution toserious pollution of natural water. #ertain silver compounds continue tohave important uses in preventing burn infections.

. =thylene oxide should be handled with care because it is explosive andcarcinogenic. It provides an effective alternative to heat sterili9ation.+I. C*$"ic %! r$ co""on%' u!$d ! )r$!$r# ti#$!.+II. R di tion+. Eamma rays cause biological damage by producing hyperreactive ions.Ioni9ing radiation provides an alternative sterili9ing method to ethyleneoxide and heat and has the advantages of not significantly altering thesterili9ed material and allowing immediate use of the ob%ect without airing.,. Gltraviolet radiation damages nucleic acids. It4s use is limited to killingmicroorganisms in air and on clean surfaces.

CLASSI,ICATION AND IDENTI,ICATION O, BACTERIA

+ system for the classification of microorganisms is essential so thatmicrobiologists can keep things straight. + system of classification helpsmicrobiologists organi9e the volumes of information on the great variety of microbes into a manageable logical scheme. Ideally such a classificationsystem would also show evolutionary relationships among the

microorganisms.That is it would illustrate how one organism is related to another. The

methods of biotechnology now hold the promise of reaching the goal of anatural system of classification. + patient sick from an infectious diseasehowever does not care particularly what species of bacteria they have8theyare %ust interested in getting well. Their recovery often depends on the

proper identification of the infectious agent.KEY CONCEPTS

1. The best classification schemes group organisms that are related through

evolution and separate those that are unrelated.



2. +t the present time the classification scheme for bacteria is based not onevolution but on convenience consisting of readily determinedcharacteristics such as shape and type of metabolism.

". The most convenient method of determining the evolutionary relatedness between organisms is based on comparing the se!uence of nucleotides intheir /N+.

$. Gnexpected relationships between various bacteria have been revealed bycomparing their 1*5 ribosomal ;N+ se!uences.

). In clinical laboratories identifying the genus and species of an organismis more important than understanding its evolutionary relationship toother organisms.

SUMMARYI. Pro&%$"! in C% !!i-'ing Org ni!"!+. The primary purpose of any classification scheme is to provide easyidentification of an organism.,. The best classification schemes are based on evolutionary relatedness.#. 5pecies is the basic taxonomic unit in bacteria> species differ from oneanother in several features determined by genes.II. Pr$!$nt D ' C% !!i-ic tion Sc*$"$!+. /escriptions of bacteria are contained in a reference text ,ergey4sManual of 5ystematic ,acteriology which is published in four volumes.III. Nu"$ric % T 9ono"'

+. This techni!ue measures the relatedness between organisms bydetermining how many characteristics the organisms have in common.I+. Mo%$cu% r A))ro c*$! to T 9ono"'+. + comparison of the /N+ base composition of organisms indicateswhether or not they may be related.

1. If the E# content of two organisms differs by more than a few percent they cannot be related.

2. 7aving the same E# content does not necessarily mean that twoorganisms are related.

,. + comparison of the se!uence of bases in /N+ can help determine therelatedness of organisms. 1. Nucleic acid hybridi9ation is the most widely used and accurateway to determine how organisms are related to one another.#. +mino acid se!uence similarities in the same protein can indicaterelatedness between organisms.

1. 6nly a minute portion of the total genetic information of the cell ismeasured by this method./. /etermining the base se!uence in 1*5 ribosomal ;N+ reveals

evolutionary relationships between diverse groups of bacteria.



1. This techni!ue allows evolutionary relations to be seen betweenorganisms that are not seen by nucleic acid hybridi9ation.

2. #ertain se!uences in 1*5 ribosomal ;N+ are always found in oneof three groups of organisms andidentify the organism as belonging to the eubacteria archaebacteria or eukaryotes.

+. M$t*od! o- Id$nti-'ing B ct$ri+. The more tests that are run the more accurate the identification.,. There are four ma%or approaches& direct techni!ues culture techni!uesdetection of microbial by products and molecular biological techni!ues.#. /irect methods of identification involve microscopic examination ofspecimens without culturing the organisms.

1. Bet mounts are made.2. 5tains especially the Eram stain are useful if enough organisms

are present.". Many harmful bacteria cannot be distinguished from non(harmful

bacteria by their appearance./. #ulture techni!ues involve growing the organisms in pure culture.

1. The specimen that is cultured depends on symptoms of disease.2. #ulturing specimens may be necessary if infectious agents are

present in small numbers.". Isolated organisms can be precisely identified.

=. /etecting products of metabolism may be easier and faster than culturingthe organism.

1. ,y(products can be measured by assaying for breakdown productsof labeled energy sources.

2. This techni!ue allows faster identification of the organisms andtherefore faster treatment.@. Molecular approaches in diagnostic microbiology usually involve analysisof /N+.

1. Nucleic acid hybridi9ation between the /N+s of two organisms8

one known the other unknown8 will indicate whether or not they are related.

2. #omparison of the cleavage pattern of two /N+ samples8onefrom a known another from anunknown organism8by the same restriction en9yme will indicatewhether or not they are related.

". /N+ probes can be used to identify species of bacteria in their natural environment or after culture.

+I. Id$nti-'ing Uncu%tur &%$ Org ni!"!

+. Microorganisms that cannot be cultured can still be identified.



1. 6ne techni!ue is to copy by #; a piece of /N+ that is specific toone of the ma%or cell kingdoms:eubacteria archaebacteria or eukaryotes< and compare the se!uencenext to the signature se!uences from previously identified organisms.

2. #; technology can be used to detect the presence of a singleorganism or virus particle in anyenvironment.

PROKARYOTIC MICROORGANISMS1 EUBACTERIA ANDARCHAEBACTERIA

This text is a survey of the ma%or groups of prokaryoticmicroorganisms as outlined in the ,ergey4s Manual of 5ystematic,acteriology. In an introductory course students of microbiology come tothink of bacteria only in terms of the garden variety types such as =. coli.This would be like thinking of birds as all being sparrows. The diversity of

bacteria is not only extreme but also even beautiful. ,acteria that kill other bacteria bacteria with stalks bacteria that look like fungi and bacteria thatlive where we thought nothing could live are only a few examples of thoseintroduced in this chapter.

KEY CONCEPTS1. rokaryotes show extreme diversity in appearance growth re!uirements

and metabolism.2. 5ome prokaryotes prey on other prokaryotes.". 5ome prokaryotes can multiply only as symbionts within eukaryotic

cells.$. rokaryotes are vitally important in the recycling of carbon nitrogen

and sulfur.). +lthough they have a prokaryotic cell structure archaebacteria are

probably more closely related to eukaryotes than to eubacteria.SUMMARY

I. Pro4 r'ot$! t* t H #$ Gr "6n$g ti#$ T')$ o- C$%% W %%+. The spirochetes

1. 5pirochetes are flexible and have a spiral shape. +xial filamentscontribute to their mobility.,. +erobic motile helical or comma(shaped Eram(negative bacteria.

1. This group of spiral and comma(shaped Eram(negative bacteriahave a rigid cell wall move by means of flagella and re!uire

oxygen for growth.



2. Microaerophiles re!uire an atmosphere containing oxygen but amuch lower concentration than in air.

". ,dellovibrios prey on other Eram(negative bacteria reproducing between the cell wall and cytoplasmic membrane.#. Eram(negative aerobic bacilli and cocci

1. This large diverse group of Eram(negative bacteria ischaracteri9ed by rod or coccoid shape and aerobic growthre!uirement.2. ;hiwbium species are important in converting atmosphericnitrogen N2 to a form usable by plants :nitrogen fixation<. They livewithin the root cells of many plant species.". seudomonads often produce non(photosynthetic pigments that cancolor the medium green in home cases. They utili9e many complexorganic compounds. 5ome can use nitrate :N "'< ion as a substitutefor molecular oxygen : 2< an example of anaerobic respiration.$. +9otobacteria are soil organisms that can fix nitrogen under

aerobic conditions./. @acultatively anaerobic Eram(negative rods

1. @acultatively anaerobic Eram(negative rods grow best aerobically but can also grow anaerobically if a suitable organic substrate is present.

2. =nterobacteria include =scherichia coli universally present in thehuman intestine.

". ?ibrios and related bacteria are mostly marine organisms. 5ome possess luciferase and are luminescent.=. +naerobic Eram(negative straight curved and helical rods

1. +naerobic Eram(negative fermentative rods have various shapesand are inhibited or killed by oxygen. 5ome species inhabit the body cavities of humans.@. /issimilatory sulfate( or sulfur(reducing bacteria

1. /issimilatory sulfate( or sulfur(reducing bacteria utili9e sulfur oroxidi9ed sulfur compounds as a final electron acceptor. They areimportant in recycling sulfur .

E. The rickettsias and chlamydias1. ;ickettsias and chlamydias are generally unable to grow outsidethe cells of a host animal. They are transmitted from one host toanother by insects mites and ticks. Nucleic acid studies showrickettsias to be genetically unrelated to chlamydias.



2. #hlamydias multiply as a vegetative form and then differentiateinto an infectious form. They are a uni!ue

group lacking peptidoglycan in their cell walls.7. =ndosymbionts

1. =ndosymbionts live within the cells of eukaryotic hosts in astable association that can be beneficial to both organisms. Mitochondriaand some chloroplasts of eukaryotes probably evolved from prokaryoticendosymbionts.

2. In endosymbionts of proto9oa environmental factors can upsetthe endosymbiotic relationship leading in some cases to the death of bothhost and endosymbiont.

". Many types of endosymbionts of other eukaryotes are knownincluding endosymbionts of insects and parasitic worms.I. Eliding non(photosynthetic bacteria

1. Eliding bacteria move slowly by an unknown mechanism when incontact with a surface. They can

break down complex polysaccharides such as cellulose. 6ne speciescauses a disease of fish.L. Myxobacteria 1. The myxobacteria are gliding fruiting bacteria. They can produce

fruiting bodies macroscopic aggregation of resting cells calledmicrocysts which are more resistant to heat drying and radiation

than the vegetative cells. #hemical signals are involved ininitiating and coordinating the action of the individual cells.

. 5heathed ,acteria1. 5heathed bacteria are unbranching filamentous forms in which thefilament is enclosed in a sheath of lipoprotein(polysaccharidematerial. The sheath protects the bacteria and attaches them to solidstructures. 5heathed bacteria may form brown scum in pollutedstreams and they can plug pipes usedin sewage treatment systems.

-. +noxygenic photosynthetic bacteria 1. +noxygenic phototrophs obtain their energy from sunlight but do

not produce oxygen as a by(product of photosynthesis. They re!uireanaerobic growth conditions and a hydrogen donor other than water. Theirancestors probably predominated in the early history of the earth.M. 6xygenic photosynthetic bacteria

1. #yanobacteria are phototrophs that like algae and plants liberateoxygen during photosynthesis.



2. Their chlorophyll type and photosynthetic process are essentiallythe same as those of algae and plants but unlike these eukaryotesmany species of cyanobacteria can fix nitrogen.". +ccessory pigments called phycobiliproteins help trap light energy.

N. ,udding and or appendaged bacteria1. rosthecate and budding bacteria have pro%ections of their

cytoplasm into unusual structures. The structures function inattachment and increase area for absorbing nutrients.

. +erobic chemoautotrophic bacteria1. The chemolithotrophic bacteria can grow in the dark using an

inorganic substance as an energy source and #6 2 for a carbon source.There are four types& nitrifiers sulfur oxidi9ers hydrogen oxidi9ers andmetal oxidi9ers.

II. Pro4 r'ot$! t* t * #$ Gr "6)o!iti#$ T')$ o- C$%% W %%+. Eram(positive cocci

1. Eram(positive cocci may occur in a chainlike arrangement or inclusters. +erobic facultative and

anaerobic forms exist. 6ne group is remarkably radiation resistant.,. ;egular non(spore(forming Eram(positive rods

1. The cylindrical non(spore(forming Eram(positive rods compose agroup of mostly unicellular organisms with smooth straight outlines.2. Eenus -actobacillus8some species help protect against infectious

disease> others have essential roles in making pickles yogurt and otherfoods.#. Irregular shaped non(spore(forming Eram(positive rods

1. Irregular non(spore(forming Eram(positive rods may showmisshapen cells uneven or metachromatic staining or branchingchains of bacteria. 5napping division is common.

Su"" r' nd T$r"!2. The corynebacteria are club(shaped and may show metachromatic

staining.6ne species causes diphtheria.

". +rthrobacters help degrade pesticides in soil. Their life cycleincludes changes in shape ranging from rod to coccus and back to rod.

$. Members of the genus +ctinomyces grow as branching filamentsthat fragment into rods./. Mycobacteria

1. Mycobacteria demonstrate the acid fast staining property. Gnusualcell wall lipids make themresistant to staining by other methods and protect them against disinfectants.

2.#ertain species are responsible for tuberculosis and leprosy.

=. +ctinomycetes with aerial and speciali9ed hyphae



1. Nocardioforms are filamentous organisms that usually form aerialmycelia and fragment into bacillary forms.

2. 6ther +ctinomycetes develop spores called conidia. #onidia arenot as resistant as endospores except in the genus Thermoactinomyces.#onidia occur in sacks as in the genera @rankia and /ermatophilusgenera. 5treptomycetes and others include antibiotic(producing as wellas disease(causing forms.

III. Pro4 r'ot$! t* t L c4 C$%% W %%!+. The mycoplasmas 1. The mycoplasmas lack cell walls. They appear to have evolved

from an ancestor similar to Eram( positive bacteria. 6ne group the spiroplasmas has species with a spiralshape and motility similar to spirochetes.

I+. Pro4 r'ot$! Wit* C$%% W %%! t* t L c4 P$)tidog%'c n+. +rchaebacteria

1. +rchaebacteria are only distantly related to other prokaryotes. Theylack peptidoglycan in their cellwalls.

2. They appear to have undergone less evolutionary change thaneubacteria.

". They exist mainly today under conditions considered adverse for eubacteria.

$. There are three kinds of archaebacteria& methanogens halobacteriaand thermoacidophiles.

0. EUKARYOTIC MICROORGANISMS1 ALGAE5 ,UNGI. ANDPROTO OA

The microbial world includes eukaryotic microorganisms as well as prokaryotic microorganisms and viruses. This chapter describes the three

groups of eukaryotic microorganisms the algae fungi and proto9oa withspecial emphasis on those that cause disease. The algae are not usuallyassociated with disease except for certain types of poisoning due to toxinsthey produce. Members of the fungi can cause serious disease in plants andanimals including humans. Members of the proto9oa are responsible for diseases such as malaria which affects the lives of millions of people.

KEY CONCEPTS1. +lgae fungi and proto9oa are eukaryotic organisms and as such have

eukaryotic cell structures. Many of these organisms are microscopic.



2. +lgae are very important in the food chain and carbon cycle but are ofminor importance in causing disease in humans.

". @ungi play an important role in the decomposition of organic materials.They also cause a great deal of damage to food crops as well as othermaterials and they are responsible for some serious diseases in humans.

$. roto9oa are single(celled often motile organisms that are an important part of 9ooplankton and the food chain. 7ome species cause disease thataffect a large part of the world4s population.

SUMMARYI. A%g $+. +lgae are photosynthetic organisms that lack the complex tissuedevelopment of higher organisms.,. +lgae are classified by photosynthetic pigments.#. +lgae are found in a wide variety of habitats./. +lgae are typical eukaryotic organisms.

1. +lgal cell walls are rigid and contain cellulose.2. Microscopic algae are usually single cells but can also live as

colonies.". Macroscopic algae are multicellular with a variety of structures

such as holdfasts blades bladders and stipes.$. ;eproduction in algae can be asexual or sexual. In some algae the

generations alternate.

=. 5ome dinoflagellates produce toxins that cause paralytic shellfish poisoning.II. ,ungi+. @ungi are non(motile non(photosynthetic heterotrophic organisms.,. @ungi are primarily terrestrial and occur in a large variety of habitats.#. The terms yeast mold and mushroom refer to morphological forms of fungi.

1. easts are single cells.2. Molds are filamentous.

". Mushrooms are the large fruiting bodies of certain fungi that areoften edible.

$. /imorphic fungi exist as either yeast or mycelium depending onconditions./. #lassification in fungi is fre!uently revised. In this text they areconsidered in three groups.

1. +mastigomycota ( terrestrial fungi2. Mastigomycota ( water molds flagellated lower fungi". Eymnomycota4( the slime molds

=. @ungi cause disease in humans in four ways.



1. 5ome people experience an allergic reaction to fungi.2. =rgot and aflatoxin are two fungal poisons that seriously affect

humans.". @ungal diseases are known as mycoses.$. @ungi destroy human food supply.

@. @ungi form symbiotic relationships with a variety of otherorganisms.-ichens and mycorrhi9as are examples.E. @ungi are economically important organisms.

1. They aid in the production of foods such as cheese bread beerand wine.

2. They are a source of antimicrobial medicines.". They spoil foods and degrade organic materials.$. They cause many plant diseases.). They are used for genetic and biochemical studies.*. Eenetically engineered yeasts produce many useful compounds

such as insulin and growthIII. Proto7o+. roto9oa are microscopic unicellular organisms that lack photosyntheticcapabilities.,. roto9oan habitats are diverse but they all re!uire moisture in some form.#. #lassification of proto9oa is based on their modes of locomotion.

1. Mastigophora(flagella

2. 5arcodina(pseudopodia". 5poro9oa(flagella or nonmotile$. #iliata(cilia

/. roto9oa lack a cell wall but maintain their distinctive shape by othermeans.=. roto9oa display polymorphism by taking on different forms in differentenvironments.@. Many proto9oa take in nutrients by pinocytosis and or phagocytosisE. ;eproduction is by both asexual and sexual methods.

7. roto9oa are important as part of the food chain.I. roto9oa cause a variety of serious diseases in humans.

2. THE NATURE AND STUDY O, +IRUSES

?iruses are very different from any of the cellular organisms that wehave described for you. Their organi9ation is at the macromolecular levelseveral steps below the organi9ation of a cell eukaryotic or prokaryotic.

?iruses are little more than a few genes carried in a protein coat. They have



no metabolic machinery of their own and therefore must rely upon that of their host cell. ?iruses cannot replicate or reproduce outside of a host cell.?iruses infect both eukaryotic and prokaryotic cells. Much of our knowledge of viral replication is from studies of viral infections of bacteria.?iruses can confer new properties on their host cells.

KEY CONCEPTS1. ?iruses are a set of genes contained in a protein coat.2. In order to multiply viruses depend to varying degrees on the en9ymatic

activity of the cells they invade.". ?iruses that infect bacteria serve as excellent models for viruses infecting

animal and plant cells.$. ?iruses can replicate within cells which they lyse or they can become

integrated into host cell /N+ and confer new properties on the cells.). /ifferent viruses can infect and replicate within all kinds of cells both

prokaryotic and eukaryotic.SUMMARY

I. +iru!$!(G$n$r % C* r ct$ri!tic!+. ?iruses have several features which distinguish them from cells.

1. They are very small81 to 1 times smaller in diameter thanthe cells they invade.

2. They contain very few genes.". The nucleic acids can be either /N+ or ;N+ but never both.

$. ?iral proteins and nucleic acids replicate separately.II. +iru! Arc*it$ctur$+. ?iruses can have different shapes. 5ome are polyhedral :having many flatsurfaces<> others are helical and others are a combination of both.,. The shape of the virus is determined by the shape of its protein coat:capsid<.#. 5ome viruses have only a capsid whereas some animal viruses have alipid membrane :envelopes< surrounding the capsid.III. +iru!6Ho!t R$% tion!*i)! E9$")%i-i$d &' P* g$6B ct$ri %

Int$r ction!+. Three ma%or types of relationships are known.

1. roductive response in which more copies of virus are made and arereleased following lysis of the host cell.

2. roductive response in which the virus leaves the cell withoutlysing it.

". -atent state in which the viral nucleic acid becomes integrated intothe host chromosome.

I+. +iru! R$)%ic tion in Producti#$ In-$ction R$!u%ting in C$%% L'!i!

+. 5tep 18 hages attach to specific sites on host bacteria.



,. 5tep 28?iral nucleic acid enters the host cell> protein coatremains on the outside.#. 5tep "8 hage /N+ is transcribed se!uentially leading to

production of specific proteins./. 5tep $8 hage /N+ is replicated and phage structural proteinsare synthesi9ed independently.=. 5tep )8 hage /N+ and protein assemble to form maturevirions8the maturation process.@. 5tep *8?irions are released from the host cell by lysis of

bacterial cell wall.+. P* g$ Gro t*(A On$6!t$) Gro t* Cur#$+. This procedure involves assaying the number of virions inside andoutside the bacteria at various times after adsorption.,. 5amples are removed at various times one set is treated with chloroformthe other is not. 5amples are inoculated onto a lawn of bacteria to lyse themleading to pla!ue which represents the site at which a single phage orinfected bacterial cell has landed.+I. +ir % R$)%ic tion in L t$nt St t$+. The /N+ of temperate viruses is integrated into the host chromosome.,. Integration of phage /N+ into the bacterial chromosome occurs becauseof identical /N+ se!uences in the phage and the bacteria.#. ;epresser must function continuously to keep prophage in the integrated

state./. +ctivation of 565 repair systems destroys the represser> the phage /N+is excised and virions are produced which lyse the cells.=. -ysogens are immune to infection by the same phage.@. rophage often codes for proteins which alter the properties of the host:lysogenic conversion<.E. ?irus #an be ;eleased Bithout 7ost #ell -ysis

1. ?iruses such as filamentous phages are released without killingthe host cell. They leave the cell by

extrusion. 2. The virus is assembled as it leaves the host cell.+II Tr n!duction+ ,oth virulent and temperate phages can transfer /N+ of one host toanother host.

1.In generali9ed transduction virulent phages can transfer any part ofthe genome. 2 In speciali9ed transduction temperate phages can transfer only aspecific set of genes.



+III Ho!t R ng$ o- +iru!$!+. +ny given virus can generally infect cells of only one or a few species., -imitation in host range is due to the fact that animal and bacterialviruses must adsorb to specific receptors on the host cell surfaceI/. M$t*od! U!$d to Stud' +iru!$!+. Many eukaryotic host cells can be cultivated in the laboratory thetechni!ue of tissue culture.,. #ells from a normal vertebrate animal grow as a monolayer attached tothe surface of a flask8but for only a limited number of generations beforethey die.# ?iruses can infect multiply and lyse cells growing in a monolayerresulting in a readily observable clearing :pla!ues<./ Infected tissue culture cells undergo characteristic changes in theirappearance depending on the virus.= KuantaO assays measures the number of infective virions by their effecton different host cell systems.@ The presence of some viruses can be detected because they can cause red

blood cells to clump

+IRUSES O, ANIMALS AND PLANTS

+lthough much of the biology of bacteriophages applies to animaland plant viruses there are significant differences in viral infections of eukaryotic cells. This chapter explores some of those differences with anemphasis on animal viruses. ou will be introduced to the classification of viruses and then a description of animal virus replication. +nimal and plantviruses cause damage to their host cells in a variety of ways including tumor formation. The human immunodeficiency virus :7I?< is the causative agent

of +I/5 or the ac!uired immunodeficiency syndrome.KEY CONCEPTS

1. ?iruses are classified on the basis of their morphology si9e and the physical and chemical nature of their nucleic acid.

2. The interactions of animal viruses with their hosts are similar to theinteractions between bacteriophages and bacteria.

". The replication of viral nucleic acid depends to varying degrees on theen9ymes of nucleic acid replication of the host cell.

$. 5ymptoms of viral(caused disease result from tissue damage of the host.



). 5ome tumors in animals result from viral /N+ becoming integrated intothe host genome and coding for the synthesis of abnormal proteinswhich interfere with normal control of host cell growth.

SUMMARYI. C% !!i-ic tion Sc*$"$ o- Ani" % +iru!$!+. +nimal viruses are classified into families genera and species basedmainly on four characteristics&

1. 5i9e2. Nature of nucleic acid they contain". resence or absence of an envelope$. 5hape of virus particle

II. +iru! Int$r ction! it* Ani" % C$%%!+. Three kinds of viral(host cell interactions can be identified :

1. productive infection which results in cell lysis2. persistent infections in which the virus often buds from the cell

without killing it and". latent infections in which viral nucleic acid is integrated into the

host cell genome.III. +iru! Mu%ti)%ic tion+. The first step in infection is adsorption of the virus to the host cell.

1. +ttachment proteins of the virus bind to specific host cellreceptors.

2. The host cell is resistant if it lacks receptors to the virus.,. ?iral entry often involves fusion of the cytoplasmic membrane of the hostwith the virion envelope

1. Naked virions enter by endocytosis.#. The replication of viral nucleic acid depends to varying degrees onen9ymes of the host cell.

1. -arger viruses generally encode more en9ymes and are lessdependent on host cell en9ymes./. Maturation of virions involves self(assembly of viral component parts.

=. ?irions are released as a result of lysis of dead cells or by budding fromliving cells.

1. +nimal and plant viruses do not use lyso9yme.I+. Int$r ction! o- Ani" % +iru!$! it* T*$ir Ho!t!+. In the case of animals outcome of infection depends on many factorsindependent of the infected cell. These include defense mechanisms of thehost.,. In most cases viruses cause no obvious harm or disease.#. Most healthy humans carry a number of different viruses.



/. +cute infections result in readily observed disease symptoms thatdisappear !uickly.=. In persistent infections the virus is present for many years withoutsymptoms of disease.

1. #hronic infections are the same as persistent infections.2. 5low viral diseases are a subgroup of persistent infections in

which the disease progresses slowly and involves the central nervoussystem.@. -atent viral infections may result from integration of viral /N+ into hostcell /N+.+. +iru!$! nd Tu"or! in Ani" %!+. Tumors caused by /N+ viruses result from integration and expression of viral /N+ in the host cell.,. Tumors caused by ;N+ viruses involve the making of a /N+ copy of theviral ;N+ which is then integrated into the chromosome of the host cell.+I. M$c* ni!"! o- C$%% Tr n!-or" tion &' +iru!$!+. The integrated viral /N+ disrupts control of normal cell growth andtissue development.,. ;etroviruses integrate oncogenes which are similar to normal host genestermed protooncogenes. 6ncogene gene products probably disrupt thefunction of protooncogene gene products.+II. +iru!$! nd Tu"or! in Hu" n!

+. Three groups of /N+ viruses have been shown to cause tumors inhumans. These are the =pstein(,arr virus hepatitis , virus and the human

papillomavirus.,. There are other possible cancer(causing viruses. These include polyomavirus and adenovirus.#. + rare human leukemia is caused by a retrovirus.

1. 7uman T(cell lymphotropic virus causes a rare cancer of a specificwhite blood cell8the T(cell.+III. HI+ Di!$ !$ >AIDS?

+. 7I? disease is caused by an ;N+ virus of the retrovirus family.I/. +iru!$! t* t C u!$ Di!$ !$ o- P% nt!+. + large number of serious plant diseases are caused by viruses.,. lant viruses are spread by a variety of mechanisms.

1. lant viruses are very resistant to inactivation.2. Insects are most important for transfer.

/. In!$ct +iru!$!+. 5ome viruses can multiply in plants and insects.,. 5ome viruses are highly pathogenic for insects and are used in biological

control of insects.



/I. +iroid!+. ?iroids short single(stranded ;N+ molecules cause a variety of plantdisease.

INTERACTIONS BETWEEN HUMANS AND MICROORGANISMS

Bhen a microorganism infects a human host the outcome of thatinfection will depend on a dynamic interaction between the microorganismand the host. Bhen the host defenses ade!uately protect the host theinfection is resolved but when the infecting microorganism gets the upper hand disease occurs. Eood health free of infection is the result of thisdynamic balance and depends on several factors. These include the person4sdefenses to resist infection and disease and the factors of the microorganismthat help it overcome host defenses. This chapter explores the non(specificdefense mechanisms of people and the virulence factors that microbes use tocounter these defense mechanisms.

KEY CONCEPTS1. The resident normal flora protects humans from invasion by pathogenic

microorganisms but is also a potential source of pathogens.2. + microorganism4s ability to establish an infection depends upon a variety

of factors including :1< the ability of the microorganism to attach to a

host tissue :2< the ability of the microorganism to invade host tissues:"< the possession of toxins and :$< the state of the host defenses.

". The host resists infection by both specific and nonspecific defensemechanisms.

SUMMARYI. T*$ *o!t d$-$nd! it!$%- g in!t in# d$r! in t o '!.+. Nonspecific mechanisms include physical barriers as well as

physiological mechanisms.,. 5pecific immune response includes speciali9ed cells and proteins that

show an enhanced response to repeat infections.II. Nor" % ,%or o- t*$ Hu" n Bod'+. Normal microbial flora constitute those organisms that coloni9e the host

but do not normally produce disease.,. Microorganisms and humans form a variety of symbiotic relationships.

1. #ommensalism is an association in which one partner benefits but the other remains unaffected.

2. Mutualism refers to an association in which both partners benefit. ". arasitism refers to an association in which one organism

benefits at the expense of the other organism.



C. Nor" % -%or i! c3uir$d -ro" cont ct! it* t*$ $n#iron"$nt./. Normal flora is important to the health of the host.

1. Normal flora includes potentially harmful organisms.2. Normal flora competes for nutrients and thus may exclude

harmful organisms.". Normal flora stimulates the immune system.

=. The human(microorganism ecosystem is continually undergoing changesas a result of external factors including food antibiotics and moisture.III. M$c* ni!"! o- P t*og$n$!i!+. Infectious microorganisms can come from a variety of sources includingother humans soil air and water.,. +ttachment is usually a necessary step in the establishment of aninfection.

1. +ttachment by a microorganism does not necessarily implyinfection but is often a necessary

prere!uisite.2. The ligands of the microorganism fit in a lock(key arrangement

with a receptor on the cell surface.". /ifferent microbial strains have different ligands> different cells

have different receptors.#. The establishment of infection usually involves the invasion of hosttissues.

1. 5ome epithelial cells ingest microorganism by a processresembling phagocytosis.

2. -arge concentrations of microorganisms may permit tissueinvasion of the host tissues./. #oloni9ation is a necessary step to establishing an infection.=. 5ome pathogens can evade or thwart the work of the phagocytes.

1. hagocytosis involves attracting the phagocyte to themicroorganism engulfing it and killing it.

2. 5ome phagocytes can avoid phagocytosis because they have a

large capsule that prevents engulfment.". 5ome microorganisms can remain alive and even multiply within

the phagocytes.@. =xtracellular products enhance microorganisms ability to cause disease.

1. =xotoxins are highly toxic distinctive proteins released by certainspecies of microorganisms. Theyare destroyed by heating.

2. =ndotoxins are lipopolysaccharides from the cell walls of Eram(negative bacteria which play a



contributing role in infectious disease. They are not destroyed byheating.

". 6ther bacterial products such as phospholipase hemolysincoagulase and others play a contributing role in infectious disease.

$. Nonbacterial toxins include the neurotoxin produced byEonyaulax an alga and aflatoxin produced

by a fungus.+. Ho!t , ctor! In-%u$ncing R$!i!t nc$ to In-$ction+. #irculating and tissue leukocytes are vital to the host defenses.

1. The granulocytes include the polymorphonuclear neutrophilseosinophils and basophils.

2. The mononuclear phagocytes and MN are the ma%or phagocyticcells in the body.,. The principal events of inflammation include the following.

1. Tissue in%ury followed by the release of chemical mediators.2. ,lood vessel dilation and the increased flow of plasma together

with redness pain and heat.". Bhite blood cell migration to area of in%ury.

# ?arious non(specific antimicrobial and antiviral substances are present in body fluids including lyso9yme beta(lysin interferons and complement./. The host4s metabolic response mobili9es the body to fight infection.

1. @ever aids in the control of infection by having an adverse effect

on the growth of the microorganism and enhances microbial defensereactions.

2. Iron is removed from the circulation by phagocytic cells makingit difficult for microorganisms to grow.=. Impaired body defenses promote infectious disease.@. Eenetic factors age and stress are important in determining thesusceptibility of people to certain infections.E. 5ome pathogens live in host tissues for years held in check by hostdefenses.

IMMUNOLOGY1 THE SPECI,IC IMMUNE RESPONSE( ANTIGENS5 ANTIBODIES5

AND CELL6MEDIATED IMMUNITY

The body4s defense against infectious diseases takes two forms&nonspecific resistance mechanisms that act as barriers to infectious agents

without regard to the specific organism and specific immune responses that



do depend on the specific organism. The immune response is characteri9ed by its specificity and a memory response. The immune response re!uires thecoordination of a number of cellular and molecular events to provide

protection. It is difficult to find a starting place because the events are soclosely related. Many aspects of the immune response still remain a mystery

but from what is known it is an ama9ing and beautiful process.

KEY CONCEPTS1. The specific immune response explains why immunity to one disease

does not usually confer immunity to another.2. The specific immune response depends upon two types of lymphocytes

interacting with each other and with other cells.". The specific immune response has 'memory ' which enhances the

response and rapidly eliminates foreign substances when they arereintroduced into the body. ?accination takes advantage of this

phenomenon.$. The specific immune response can discriminate between self and nonself.

SUMMARYI. Inn t$ >N tur %? nd Ac3uir$d I""unit'+. Innate immunity confers disease resistance that does not involve the

production of antibodies or cellular immunity.

,. Naturally ac!uired active immunity comes from exposure to antigens inthe environment.#. Naturally ac!uired passive immunity involves the transfer of antibodiessuch as a mother to her fetus./. +rtificially ac!uired active immunity involves vaccination.=. +rtificially ac!uired passive immunity involves preformed antibodiessuch as immune globulin.II. T*$ Non!)$ci-ic +$r!u! t*$ S)$ci-ic I""un$ R$!)on!$+. Nonspecific defenses include physical and physiological barriers and are

found in most of the animal world.,. 5pecific immune response has four features&1. Two sets of lymphocytes involved.2. ;esponse is highly specific.". ;esponse has memory.$. ;esponse is capable of discriminating between self and nonself.III. Antig$n!+. +ntigens are usually macromolecules.,. +ntigens are usually foreign to the host.

#. The immune response is directed against antigenic determinants.



/. 7aptens must bind to larger antigenic molecules to induce an immuneresponse.=. Most antigens must be processed by antigen(processing cells before theycan be involved an immune response.@. Most antigens must be associated with products of the ma%orhistocompatibility complex :M7#< in order to cause an immune response.I+. T*$ Du %it' o- t*$ S)$ci-ic I""un$ R$!)on!$+. The humoral immune system.

1. Includes the blood lymph and mucus secretions.2. -ymphocytes known as , cells produce antibodies.

,. The cell(mediated immune system.1. -ymphocytes known as T cells.2. T cells do not secrete antibodies but act directly on other cells.

+. B C$%%! nd t*$ Anti&od' R$!)on!$+. +ntibody molecules are proteins known as immunoglobulins.,. +ntibody molecules have a shape with antigen reaction sites at the endsof the arms of the#. Eenes coding for different antibodies achieves antibody diversity throughdeletions and rearrangements of genetic material in germline cells./. +ntigen(antibody relationships can be likened to a lock and key.=. There are five classes of immunoglobulins&

1. IgE is present in the greatest amount and only one that crosses

the placenta to protect the fetus and newborn.2. IgM first antibody to form.". Ig+ is found mainly on mucous surfaces.$. Ig/ serves as a specific membrane receptor on ,(cells.). Ig= is implicated in allergic reactions.

@. Memory cells remain much longer and are primed to respond !uickly toantigen.E. +ntibody can cause opsoni9ation thereby promoting phagocytosis.+I. T c$%%! nd C$%%6"$di t$d I""unit'

+. It is the T cell receptor that interacts specifically with the antigenicdeterminants.,. There are three subpopulations of T cells&

1. 7elper T cells work with , cells to form an antibody response.2. #ytotoxic T cells kill virus(infected cells and tumor cells.". 5uppressor cells help regulate the immune response.

#. 6ther cells are also involved in cell mediated immunity.1. iller cells.2. Mononuclear phagocytes and macrophages.



+II. T*$ Co""on %t' o- t*$ T o Di#i!ion! o- t*$ S)$ci-ic I""un$R$!)on!$

+. , and T cells have antigen recognition sites on their cell membranes.,. +n immune response is triggered if the antigen and recognition site havea close fit.#. =ach individual lymphocyte has only a single type of antigen recognitionsite./. The immune response depends on clonal expansion of antigenicallystimulated lymphocytes.=. 5ome lymphocytes are live a long time as memory cells ready to

participate in an enhance immune response.+III. T*$ S$cond r' >An "n$!tic? R$!)on!$ nd + ccin tion+. The anamnestic response depends on memory cells.,. ?accines are made by inactivation of viruses or by attenuation of virusesor microorganisms.I/. I""uno%ogic % To%$r nc$+. ;ecognition of self by the immune system occurs during fetaldevelopment.,. -ymphocytes able to bind to self antigens are eliminated before birth./. R$gu% tion o- t*$ I""un$ R$!)on!$ Co"$! -ro" Su))r$!!or C$%%! !W$%% ! ,$$d& c4 M$c* ni!"!.

IMMUNOLOGY1 DISORDERS O, THE IMMUNE SYSTEM

+ healthy effectively functioning immune system is a beautifulthing. Its beauty is because it is a very complicated thing that re!uires thecoordination of many individual parts to protect against infection.5ometimes portions of the system fail and the results can be moredetrimental than useful. Bhen the system fails to respond ade!uately to

antigenic stimulation an immunodeficiency occurs. This failure may be aninherited defect or ac!uired as in +I/5. +t times our immune systemappears to over(react to antigenic stimulation and instead of protecting usagainst certain antigens it actually causes damage to us. This is the situationknown as hypersensitivity or allergies. @inally in autoimmunity our immune systems may fail to recogni9e our own body antigen as self and

begin to produce antibodies against our own tissue antigens. +ll threeconditions can have very serious and sometimes devastating effects.

KEY CONCEPTS



1. Immunodeficiency results when the immune system cannot respondade!uately to antigenic stimulation.2. 7ypersensitivities result from the immune system reacting inappropriatelyto certain antigens.". +utoimmune disease results from the immune system of the bodyresponding to its own tissues as foreign.$. + number of diagnostic tests rely on immune responses to antigens.

SUMMARYI. I""unod$-ici$nc' Di!$ !$!+. rimary immunodeficiency disease.

1. 6ccurs because of genetic defect.2. In /iEeorge syndrome the thymus fails to develop and patient

lacks T lymphocytes.". P(linked agammaglobulinemia patients lack , lymphocytes.$. In severe combined immunodeficiency disease the bone marrow

stem cells are defective.). #hediak(7igashi disease affects the phagocytes.

,. 5econdary immunodeficiency disease.1. +c!uired as the result of infection aging or other factors.2. Multiple myelomas are cancers.". +c!uired Immune /eficiency /isease :+I/5<a. #aused by 7I? virus a retrovirus.

b. ?irus kills T(helper lymphocytes.c. ,ody susceptible to opportunistic infections.

II. H')$r!$n!iti#iti$!+. Type I hypersensitivity is an Ig=(mediated reaction.

1. Ig= antibodies attach to receptors on mast cells and basophils. 2. Bhen antigen combines with these cell(fixed Ig= antibodieshistamine and other chemical mediators are released.

". Ig=(mediated skin reactions such as hives are produced.$. -ocali9ed anaphylaxis such as hayfever and asthma are Ig=(

mediated respiratory reactions.). Eenerali9ed anaphylaxis can occur after a bee sting or penicillin

reaction.*. Immunotherapy involves repeatedly in%ecting a small but

increasing amount of the offending antigen in order to elicit an IgEresponse.,. Type II hypersensitivity or cytotoxic reactions are caused by humoralantibodies that destroy normal cells.

1. #omplement(fixing antibodies react with cell surface antigens and

cause in%ury or death to cells.



2. Transfusion reactions.a. +,6 blood group system.

b. +,6 antigens are polysaccharides on the red blood cells.". 7emolytic disease of newborns.

a. ;h or :rhesus< blood group system is involved. b. If an ;h(negative mother carries an ;h(positive fetus the ;h( positive cells cause antibody production inthe mother. These antibodies can cross the placenta and destroyfetal red blood cells.c. + new treatment involves in%ecting anti(;h antibodies into themother shortly after delivery or abortion

to develop anti(;h antibodies.#. Type III hypersensitivity or immune complexes activate inflammatorymechanisms

1. Immune complexes have considerable biological activity such as blood clotting mechanisms attraction of polymorphonuclear leukocytes and stimulation of lysosomal en9yme release.

2. Immune complexes can be deposited in kidneys %oints and skin.". +rthus reaction is the death of tissue following in%ection of

antigen into previously immuni9ed animal.$. 6ther diseases such as serum sickness and farmer4s lung involve

immune complexes./. Type I? 7ypersensitivity or /elayed 7ypersensitivity involves T cellsand cell(mediated immunity.

1. The response develops slowly over a few days.2. Tuberculin skin test is an example of delayed hypersensitivity.". #ontact allergies are reactions to metals poison ivy and other

substances.$. /elayed hypersensitivity is involved in infectious diseases.

a. -eprosy and hepatitis are examples.

b. #ell destruction with impairment of tissue function is involved.=. +ntigenic incompatibility leads to tissue graft re%ection. 1. M7# matching essential to avoid re%ection. 2. Gse of immunosuppressant drugs such as cyclosporin hashelped keep graft re%ection under control. ". Immunity to cancer cells sometimes breaks down.III. Autoi""un$ Di!$ !$!+. 5ome such as myesthenia gravis are due to the production of humoralantibodies



,. 5ome such as sympathetic ophthalmia are due to delayedhypersensitivity reactions.I+. I""uno%ogic % Di gno!tic T$!ting T$c*ni3u$!+. recipitation reactions including the 6uchterlony techni!ue and immuneelectrophoresis involve soluble antigen.,. +gglutination reactions are similar to precipitin reactions except theyinvolve particulate antigen.#. #omplement fixation test uses antibody(sensiti9ed red blood cells todetect the presence of complement and cause cell lysis./. ?irus neutrali9ation test.=. /irect and indirect immunofluorescence tests.@. ;adioimmunoassay :;I+< and en9yme(linked imunosorbent assay:=-I5+<

=. EPIDEMIOLOGY AND PUBLIC HEALTH

=pidemiology is the study of factors that influence the fre!uency anddistribution of diseases. =xactly what does that meanQ It means thatepidemiologists are like detectives because they try to predict when anepidemic is occurring or is going to occur. They look for clues related to the

number of new cases of a disease compared to its usual numbers. They look for clues as to where the epidemic started where it will spread and who aremost likely to get the disease. @rom this information public health servicescan try to interrupt the transmission of the disease by appropriate means.=pidemiologists need a lot of math and statistical training in addition tomicrobiology.

KEY CONCEPTS

1. Today4s public health system depends on advanced technology socialorgani9ation and political stability.

2. Identifying the origin of an epidemic depends on a careful comparison ofthe characteristics and activities of those affected and unaffected by theepidemic.

". /ifferent infectious agents can produce the same symptoms and the sameinfectious agent can produce different symptoms.



$. /ifferent strains within the same species of potential pathogen can differ markedly in virulence and pathogenicity.

). +symptomatic carriers of an infectious agent can be responsible for epidemics.

*. In epidemics where most infections are asymptomatic the extent ofspread of the causative agent can be far greater than indicated by thenumber of ill people.

. Infectious agents with a long incubation period can spread widely beforean epidemic is detected.

0. The smaller the infecting dose of a pathogen the longer the incubation period and the greater the likelihood of asymptomatic infection.

SUMMARY

I. E)id$"io%og' I! t*$ Stud' o- , ctor! In-%u$ncing t*$ ,r$3u$nc' ndDi!tri&ution o- Di!$ !$+. +n epidemic is an unusually large number of cases in a

population.,. 5poradic cases representing the usual incidence is known asendemic.#. + pandemic is a world wide epidemic.

II. In-$ctiou! Di!$ !$ E)id$"ic!5 Origin nd S)r$ d+. The cause or origin is determined by first defining the characteristics ofthe people :population< involved.,. The infectious agent must be precisely identified.

1. ,acteriophage typing is based on viral specificity8 Staphylococcus.

2. ,acteriocin typing8 Pseudomonas species.". +ntibiograms.$. ,iotyping and serotyping.

). =lectrophoresis of endonuclease digests8herpes simplex virus.#. The reservoir of an infectious agent is the sum of its potential sources./. @actors in the spread of epidemics.

1. ?ectors and vehicles.2. Gse of sentinels.". Incubation period.

=. +irborne spread of infectious disease.@. @ood and water in the transmission of infectious disease

1. Multiplication of the pathogen in food.



2. -ong incubation and asymptomatic infections with water(bome pathogens.E. erson(to(person transmission.

1. #ontamination of hands by fomites respiratory secretions feces.

2. #arriers.

III. Po)u% tion C* r ct$ri!tic!+. +ge8prior exposure.,. Eenetic background8malaria resistance among black people.#. Nutrition crowding and cultural factors.

I+. T*$ In-$cting Ag$nt+. Microbial virulence8bacterial meningitis.

,. Intensity of exposure8role of the infectious dose.

+. A))ro c*$! to Contro% o- In-$ctiou! Di!$ !$!+. romotion of good general health.

1. +de!uate rest nutrition exercise freedom from stress.2. +ctive immuni9ation.

,. ;educing the reservoir and interrupting transmission.

+I. Ho!)it % E)id$"io%og'+. Nosocomial infections.

1. Gnusually susceptible population.2. resence of virulent pathogen.". #arriers among hospital staff.$. otential of disease transmission to the outside community.

,. 7ospital epidemiologist.

+II. In-$ctiou! Di!$ !$ Contro% N$t or4

+. 5chools microbiology laboratories news media.1. Eovernmental public health laboratories.,. National #enters for /isease #ontrol and revention and the Borld7ealth 6rgani9ation.

1. 5tudies.2. Infection control teams.". +ssistance to laboratories.



ANTIMICROBIALAND ANTI+IRAL MEDICINESTreatment of infectious disease has obviously been a primary goal of

medicine for centuries. aul =hriich4s search for the 'magic bullet' that

would kill an infectious agent without harming the patient was a systematicapproach to the problem of antimicrobial therapy. The approach to thediscovery of new antimicrobial agents today applies the knowledge of metabolism and genetics to solving the problem. +ntimicrobial agents thatinterfere with processes uni!ue to the pathogen will have the highesttherapeutic index. Bhile there are a considerable number of antimicrobialagents available they fall into a few categories based either on their structure and or their activity. This chapter summari9es the ma%or groups of

antimicrobial agents their activity and application.KEY CONCEPTS

1. #ertain chemicals selectively kill or inhibit the growth of one organismwhile sparing another.

2. Most antimicrobial medicines exploit the differences that are found between prokaryotic and eukaryotic cell structure and metabolism.

". -aboratory tests of the susceptibility of microorganisms to antimicrobialmedicines help predict the effectiveness of the medicines in vivo.

$. Mutations and transfer of genetic information have allowedmicroorganisms to develop resistance to each new antimicrobialmedicine that has been developed.

). =n9ymes uni!ue to viral replication provide potential sites of chemotherapeutic action.

*. +ntiviral substances normally produced by the human body can now be produced in vitro and used in antiviral therapy.

SUMMARY

I. Anti"icro&i % C*$"ot*$r )' D$)$nd! on t*$ Princi)%$ o- S$%$cti#$To9icit'II. Anti&iotic! Ar$ Anti"icro&i % Su&!t nc$! Produc$d W*o%%' or inP rt &' C$rt in B ct$ri nd Mo%d!+. #hemical modification of antibiotics has produced families of antimicrobial medications having different properties.

III. Anti& ct$ri % M$dicin$!+. 5ynthetic medicines include sulfa drugs trimethoprim isonia9id andothers.

,. +ntibiotics include beta(lactams tetracyclines erythromycinlincomycins aminoglycosides polypeptides and rifamycins.



I+. Mod$! o- Action o- Anti"icro&i % M$dicin$!+. #ompetitive inhibition involves reversible impairment of an en9yme by asubstance resembling the en9yme4s normal substrate.,. ,eta(lactams and certain other antibiotics act by impairing bacterial cellwall synthesis.#. 5elective inhibition of microbial protein synthesis depends on differences

between eukaryotic and prokaryotic ribosomes./. + few antimicrobial agents are active against cytoplasmic membranes.=. ;ifampin and the !uinolones selectively inhibit bacterial nucleic acidsynthesis.

+. B ct$ri % S$n!iti#it' T$!ting nd It! R$% tion!*i) to Anti"icro&i %L$#$%! in Bod' ,%uid!

+. 5usceptibility to antibacterial medicines can be !uantified by determiningminimal inhibitory concentrations.,. The terms sensitive and resistant refer to whether a microorganism islikely to be treatable or not.+I. Li"it tion! on t*$ + %u$ o- Anti& ct$ri % Ag$nt!+. + progressive increase in the percentage of resistant strains has occurredfollowing the introduction of each new antimicrobial.

1. 5election of 'wild' resistant variants.2. ;ole of gene transfer in resistance.". ;ole of environment in resistance.$. Mechanisms of resistance include en9ymatic inactivation of the

antimicrobial medication decrease in permeability to the medication andchanges in the target substance so that it no longer binds the medication.,. Toxins and host factors may also limit antimicrobial effectiveness.

+II. M$dicin$! t* t Act Ag in!t Eu4 r'otic P t*og$n!

+. @ungi.1. /eep infections.2. 5uperficial infections.

,. roto9oa.

+III. M$dicin$! Acti#$ Ag in!t +iru!$! Inc%ud$ A" nt din$5 Ac'c%o#ir5,o!c "$t5 Purin$ nd P'ri"idin$ An %og!5 nd Int$r-$ron

1. +mantadine prevents influen9a + by interfering with viral uncoating.

2. 5everal base analogs inhibit reverse transcriptase.". Interferons interfere with translation of viral messenger ;N+.



MICROBIAL ECOLOGY AND TERRESTRIAL MICROBIOLOGY

Be usually think of dirt as being a place of filth and infection> and itdoes contain a number of pathogenic organisms. 7owever the microbial

populations of the soil are staggering both in number and in variety. Thenature of the soil is dependent on its microbial populations. Microorganismsin the soil provide nutrients in their proper form to plants by processesranging from nitrogen fixation to decomposition. + number of conditions ofthe microenvironment in turn influence the growth and well(being of themicrobial population. 5oil is a dynamic living community. Microorganismsare even responsible for the sweet fresh smell of the soil that we soappreciate in the spring after a very hard sterile winter.

KEY CONCEPTS1. @or the microorganism the environment immediately surrounding itits microenvironment is most important.2. /ifferent microorganisms are capable of growing in a wide variety of

environments but each will grow best in those environments for whichit is well adapted.

". The variety of microorganisms found in the soil is influenced by its physical nature and the available nutrients.

$. The microorganisms of the soil are essential in recycling the biologically important elements oxygen nitrogen carbon sulfur and phosphorus.

SUMMARYI. Princi)%$! o- Micro&i % Eco%og'+. The ma%or subunits of the biosphere are the ecosystems.,. Microenvironments are the most important considerations for bacterial

cells.#. Microbial competition demands rapid reproduction and efficient use of

nutrients./. Microorganisms can both cause and adapt to environmental changes asin antibiotic resistance and souring of milk.=. 6ligotrophs are organisms that can grow in very low nutrientenvironments.II. Microorg ni!"! nd Soi%+. 5oil is a complex substance composed of both organic and inorganicmaterials.,. 5oil teems with a variety of life forms including bacteria algae fungi

proto9oa nematodes worms and other eukaryotic organisms.



III. En#iron"$nt In-%u$nc$! t*$ + ri$t' o- Org ni!"! t* t Ar$Pr$!$nt in Soi%+. Moisture in the soil affects the oxygen supply.

1. Baterlogged soils primarily support anaerobic organisms.2. ;elatively few organisms grow in desert climates.

,. 7ighly acid conditions inhibit the growth of most bacteria. @ungi generallyare more tolerant of both high and low p7.#. Temperature regulates both the microbial metabolic activity rate as well

as the type of organism that can grow.1. Most bacteria are mesophiles and grow between 2 F# and ) F#.2. sychrophiles grow below 2 F#.

". Thermophiles grow above ) F#./. The availability of organic matter tends to limit the si9e of

the heterotrophic microbial population.I+. Bioc*$"ic % C'c%ing+. The organisms involved in recycling can be divided into three groups&

the producers the consumers and the decomposers. ,. +ll ecosystems must have energy added to them usually in the

form of sunlight. #. 6xygen cycles between respirers and photosynthesi9ers. /. #arbon cycles between organic compounds and carbon dioxide.

1. roducers fix atmospheric # 2 into organic compounds.

2. /ecomposers use organic material as a source ofcarbon for various biological processes.

=. Nitrogen cycles between organic compounds and a variety of inorganic compounds.

1. +mmonification involves the degradation of cell componentssuch as proteins to # 2 ammonium and sulfate ions and waterthrough a series of steps.

2. Nitrification is the microbial oxidation whereby ammonium isconverted to nitrite and then to nitrate.

". /enitrification occurs when some anaerobic bacteria usenitrate as a final electron acceptor resulting in the liberation of

N2 and the loss of nitrogen to the ecosystem.$. Nitrogen fixation involves prokaryotic microorganisms thatare capable of reducing nitrogen gas to ammonium ion that isthen used as the amino group of amino acids. 6xygen(sensitiveen9ymes called nitrogenases are responsible for nitrogen fixation.5ome of these bacteria are free(living while others must establisha symbiotic relationship with plants.



@. hosphorus also cycles between organic and inorganiccompounds.E. The sulfur cycle involves several important types of organisms.

+. Micro&i % D$co")o!ition o- S'nt*$tic C*$"ic %!+. Most naturally occurring organic compounds are

degraded by some microorganism. ,. 5ome synthetic compounds are not readily degraded.

1. /6T2. 2 $ )(T". #,s

MICROBIOLOGY AND ECOLOGY O, A UATICEN+IRONMENTS

Nearly all water contains microorganisms of some type. +!uaticenvironments range from extremely hypertonic :salty< such as the Ereat 5alt-ake to nearly pure distilled water stored in plastic carboys. Microorganismslive in the entire range of a!uatic environments. Most environments havetheir own natural populations of organisms as well as many that arecontaminated from outside sources such as sewage. This chapter looks at thenature of a!uatic environments and the organisms that inhabit them as well

as the effects of pollution on a!uatic environments.KEY CONCEPTS

1. ,ecause water is an excellent solvent many otherwise usefulsubstances can adversely affect its !uality.2. @actors such as temperature p7 and dissolved minerals determinewhich microorganisms can live in water.". The available nutrients in water determine the variety ofmicroorganisms that can live in it.

SUMMARY

I. T*$ N tur$ o- A3u tic En#iron"$nt!+. Bater is an extremely efficient solvent and most water is a dilute

solution of any number of substances. ,. ;ain water usually has few impurities.

1. +cid rain occurs because of air pollution.2. -akes and streams can be seriously affected by acid rain.

#. The properties of water depend on where the water comes from orwhat it passes through. /. @reshwater environments are diverse.



1. =utrophication of freshwater occurs when nutrients are added tothe water.

2. These nutrients cancome from humanactivities.

=. Marine environments differdepending on their proximity toand.

1. 6pen oceans are nutrient poor.2. =stuaries are rich in nutrients.

II. T*$ Micro&i % ,%or o- A3u tic En#iron"$nt!+. The microbial population of freshwater is

dictated by the available nutrients.,. 5eawater contains different microbial

species than freshwater.1. 7ydrostatic pressure determines which organisms can survive.2. It is difficult to measure organisms in seawater because they are

so sparse.III. T*$ Con!$3u$nc$! o- W t$r Po%%ution+. ollution with pathogenic organisms can cause disease epidemics.,. =utrophication of freshwater by human pollution is an important

problem that can be reversed.I+. Microorg ni!"! nd Po%%ution

MICROBIOLOGY O, WASTE TREATMENT

The treatment of our household and industrial waste is a problem thatliterally grows larger each day. The not too dissimilar threat of cholera wasthe driving force behind the development of sewage systems in the last

century. Today our environment and possibly again our health is beingthreatened by the wastes that we are producing. Be are developing newsolutions to help solve these problems but they at first appear expensiveuntil we seriously consider the cost if we do nothing. The good news is thatindividuals can do something to help. #omposting by individuals willremove some 2 (" A of the burden of solid waste disposal.

KEY CONCEPTS1. roper sewage treatment is necessary to ensure the health of thecommunity.



2. roper sewage treatment depends on the stabili9ation of wastes bymicroorganisms.". athogenic bacteria are usually eliminated by the secondary sewagetreatment process.$. Innovations such as trickling filters and artificial wetlands are goodsolutions to small scale sewage treatment problems.). ,oth backyard and commercial composting reduce the need for largelandfills for disposal of solid waste.

SUMMARYI. T*$ Micro&io%og' o- W !t$ Tr$ t"$nt

+. 5ewage contains a variety of substances.1. 7uman wastes.2. Industrial wastes.". @ood wastes.

,. Microorganisms degrade the componentsof sewage to inorganic compounds. #. Microorganisms reduce the

biological oxygen demand :,6/<of sewage.

1. rimary treatment.2. 5econdary treatment.". Tertiary treatment.

/. 5ewage can also be treated on a small scale using lagooningtrickling filters septic tanks and artificial wetlands. =. Gsing treated waste residues is still a problem.

II. Micro&io%og' o- So%id W !t$ Tr$ t"$nt+. 5anitary landfills have been a low(cost method for disposingof solid waste.,. ;ecycling programs and other means are being used toreduce the amount of garbage going into landfills.#. ,ackyard and commercial composting both help reduce the

amount of material in landfills and help add nutrients to the soil.

THE MICROBIOLOGY O, ,OOD AND BE+ERAGES

There is both good news and bad news concerning the activities of microorganisms in food and beverages. The bad news i that microorganismsare responsible for the spoilage of food. Bhen this spoilage prevents food

from being used in a world many starving people the loss is tragic. Be



usually however measure the loss in terms of dollars and it can beextensive. The good news is that microorganisms are also responsible for many of our fine and delicious foods. In some respects this food productionis actually controlled spoilage. Many of our fermented foods were producedinitially because the fermentation also preserves them. nowing what spoilsfood can teach us how to preserve it.

KEY CONCEPTS1. + variety of microorganisms can use human food as a growthmedium degrade it and spoil it for human consumptio2. @ood spoilage can be eliminated or retarded by altering the conditionsunder which microorganisms gRow.". 7eating drying refrigerating free9ing irradiating and adding

chemicals are some of the ways to control the growth Rmicroorganisms on food.

$. + variety of foods such as bread cheese and alcoholic beveragesresult from metabolic activities of microorganisms.

SUMMARYI. Microorg ni!"! Ar$ R$!)on!i&%$ -or ,ood S)oi% g$

+. @ood spoilage microorganisms are usuallynonpathogenic for humans.

,. Pseudomonas species are the most commonfood spoilage organisms.

#. @ood poisoning is often caused byStaphylococcus aureus.

II. S)oi% g$ Org ni!"!R$3uir$ S)$ci-icCondition! to Gro +. Bater activity.,. p7.#. +vailability of

nutrients.

III. Prot$ction o- ,ood &' N tur %%' Occurring Anti"icro&i %Su&!t nc$!I+. ,ood Pr$!$r# tion

+. @ood contaminants can be killed by high(temperature treatment.1. The primary concern is the destruction of Clostridium

botulinum spores.2. The higher the temperature the less time is needed.". The more microorganisms present the longer the time and the

higher the temperature re!uired.



$. The condition of the microorganism and the type ofenvironment is important to know.,. asteuri9ation kills many potentially pathogenic organisms but

does not sterili9e the food.#. Erowth of spoilage organisms is slowed or halted by low(

temperature treatment.1. -ow temperatures such as a refrigerator slow the growth of

organisms but do not kill them.2. @ree9ing stops the growth ofmicroorganisms but may not kill them.

/. /esiccation or drying prevents microbial growth byreducing the water activity.

1. /rying stops the growth of bacteria but does not kill all bacteria.2. 5ugaring salting and smoking also act to reduce the amount ofwater in foods.". -yophili9ation is free9e(drying.

=. #hemicals are added to food for preservation. @. Irradiation can beused for some food preservation but thus far has limited use.

1. Microwaves.2. Eamma irradiation.

+. Contro% o- Micro&i % H 7 rd! in ,ood+. The Gnited 5tates has strict standard of control.

,. @ood(borne illnesses occur in spite of these strict controls.1. @ood(borne infections.

2. @ood( borneintoxications.

#. 5ome diseases aretransmitted through food.

+I. Micro&$! Ar$ U!$d in t*$

Production o- ,ood ndB$#$r g$!.

+. Milk products are made usinglactic acid bacteria.

1. ogurt2. #heese

,. ickles and sauerkraut are also made usinglactic acid bacteria.

#. 5oy sauce is traditionally made by fermenting

soy beans.



/. ,read is produced with the yeastSaccharomyces cerevesiae.

=. +lcoholic beverages are produced by fermentationusually with Saccharomyces.

1. Bine S grapes and other fruits are fermented to produce wines.2. ,eer is made by fermenting starch.". /istilled spirits.$. ?inegar is made by Acetobacter and Gluconobacter speciesoxidi9ing alcohol to acetic acid.



*$

Microbiology General

Documents

Transcript of Microbiology General